vignettes/SampleCodeForNeoantimon.md
In hase62/Neoantimon: Neoantimon: A multifunctional R package for identification of tumor-specific neoantigens
title: "SampleCodeForNeoantimon"
author: "T. Hasegawa"
date: "2024/6/12"
output:
pdf_document: default
html_document: default
```{=html}
## Data Preparation and Sample Codes for Analysis
``` r
#install.packages('devtools');
library(devtools);
## Loading required package: usethis
install_github('hase62/Neoantimon');
## Skipping install of 'Neoantimon' from a github remote, the SHA1 (2ed545f8) has not changed since last install.
## Use `force = TRUE` to force installation
library(Neoantimon);
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("biomaRt")
## Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 (2024-04-24)
## Warning: package(s) not installed when version(s) same as or greater than current; use
## `force = TRUE` to re-install: 'biomaRt'
library(biomaRt)
To calculate the binding affinity of neoantigen candaites, which are generated from from SNVs, to HLA ClassI. When using MHCflurry, [[1]] and [[2]] include the results of NetMHCpan and MHCflurry, respectively.
Result_HLA1_SNV <- MainSNVClass1(input_annovar_format_file = "./../data/sample_vcf.annovar.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c1.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCpan_dir = "./../lib/netMHCpan-4.1/netMHCpan",
depth_tumor_column = 12,
depth_normal_column = 14,
SNPs = "./../data/sample_vcf.snps.txt",
multiple_variants = TRUE)
## [1] "HLAtype: A*02:01" "HLAtype: A*32:01" "HLAtype: B*15:17" "HLAtype: B*51:01"
## [5] "HLAtype: C*07:01" "HLAtype: C*15:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Set depth_normal_column as 14 depth_normal"
## [1] "Set depth_tumor_column as 12 depth_tumor"
## [1] "Set nm_id_column as 10 AAChange.refGene"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tGeneDetail.refGene\tExonicFunc.refGene\tAAChange.refGene\tcytoBand\tdepth_tumor\tvariantNum_tumor\tdepth_normal"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
## [1] "Start Analysis: Mutation 1"
## [1] "NM_001358 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 2"
## [1] "NM_002048 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 3"
## [1] "NM_006205 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.txt.list.vcf"
## [1] "Executing netMHCpan to result.ID.SNV1"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a HLA-A02:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.1.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a HLA-A32:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.2.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a HLA-B15:17 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.3.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a HLA-B51:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.4.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a HLA-C07:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.5.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a HLA-C15:02 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.6.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a HLA-A02:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.1.wtpeptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a HLA-A32:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.2.wtpeptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a HLA-B15:17 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.3.wtpeptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a HLA-B51:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.4.wtpeptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a HLA-C07:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.5.wtpeptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a HLA-C15:02 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.6.wtpeptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.1.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.2.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.3.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.4.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.5.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.6.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA1_SNV <- CalculatePriorityScores(result = Result_HLA1_SNV, useRNAvaf = FALSE)
print(head(Result_HLA1_SNV))
## HLA Pos Gene Evaluated_Mutant_Peptide Mut_EL Mut_Rank
## [1,] "HLA-A*02:01" "2" "0_DHX15" "ERDYLEAAIRA" "0.0001110" "39.889"
## [2,] "HLA-A*02:01" "3" "0_DHX15" "RDYLEAAIRAV" "0.0093530" "6.946"
## [3,] "HLA-A*02:01" "4" "0_DHX15" "DYLEAAIRAVI" "0.0003140" "27.742"
## [4,] "HLA-A*02:01" "5" "0_DHX15" "YLEAAIRAVIQ" "0.0004340" "24.625"
## [5,] "HLA-A*02:01" "6" "0_DHX15" "LEAAIRAVIQI" "0.0001100" "40.000"
## [6,] "HLA-A*02:01" "7" "0_DHX15" "EAAIRAVIQIH" "0.0000070" "78.333"
## Evaluated_Wt_Peptide Wt_EL Wt_Rank Chr NM_ID Change Ref
## [1,] "ERDYLEAAIRT" "0.0000310" "58.182" "4" "NM_001358" "c.A1012G" "T"
## [2,] "RDYLEAAIRTV" "0.0192400" "4.851" "4" "NM_001358" "c.A1012G" "T"
## [3,] "DYLEAAIRTVI" "0.0003800" "25.878" "4" "NM_001358" "c.A1012G" "T"
## [4,] "YLEAAIRTVIQ" "0.0009320" "18.339" "4" "NM_001358" "c.A1012G" "T"
## [5,] "LEAAIRTVIQI" "0.0001630" "35.077" "4" "NM_001358" "c.A1012G" "T"
## [6,] "EAAIRTVIQIH" "0.0000080" "76.667" "4" "NM_001358" "c.A1012G" "T"
## Alt Prob Mutation_Prob. Exon_Start Exon_End Mutation_Position
## [1,] "C" "0" "0" "24529097" "24586177" "4_24556416"
## [2,] "C" "0" "0" "24529097" "24586177" "4_24556416"
## [3,] "C" "0" "0" "24529097" "24586177" "4_24556416"
## [4,] "C" "0" "0" "24529097" "24586177" "4_24556416"
## [5,] "C" "0" "0" "24529097" "24586177" "4_24556416"
## [6,] "C" "0" "0" "24529097" "24586177" "4_24556416"
## Total_Depth Tumor_Depth Wt_Peptide
## [1,] "294" "143" "PERDYLEAAIRTVIQIHMCEEEE"
## [2,] "294" "143" "PERDYLEAAIRTVIQIHMCEEEE"
## [3,] "294" "143" "PERDYLEAAIRTVIQIHMCEEEE"
## [4,] "294" "143" "PERDYLEAAIRTVIQIHMCEEEE"
## [5,] "294" "143" "PERDYLEAAIRTVIQIHMCEEEE"
## [6,] "294" "143" "PERDYLEAAIRTVIQIHMCEEEE"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA
## [1,] "PERDYLEAAIRAVIQIHMCEEEE" "1.35204" "NA" "NA"
## [2,] "PERDYLEAAIRAVIQIHMCEEEE" "1.35204" "NA" "NA"
## [3,] "PERDYLEAAIRAVIQIHMCEEEE" "1.35204" "NA" "NA"
## [4,] "PERDYLEAAIRAVIQIHMCEEEE" "1.35204" "NA" "NA"
## [5,] "PERDYLEAAIRAVIQIHMCEEEE" "1.35204" "NA" "NA"
## [6,] "PERDYLEAAIRAVIQIHMCEEEE" "1.35204" "NA" "NA"
## Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max
## [1,] "0.657624897959184" "NA" "NA" "NA"
## [2,] "0.657624897959184" "NA" "NA" "NA"
## [3,] "0.657624897959184" "NA" "NA" "NA"
## [4,] "0.657624897959184" "NA" "NA" "NA"
## [5,] "0.657624897959184" "NA" "NA" "NA"
## [6,] "0.657624897959184" "NA" "NA" "NA"
## P_I P_R P
## [1,] "0.28500874209118" "3.02670563878825e-83" "2.25864121245377e-83"
## [2,] "0.285008765600042" "1.03701641904894e-11" "7.73860527445574e-12"
## [3,] "0.285008742435297" "7.20851064695389e-57" "5.37926087656814e-57"
## [4,] "0.28500874345477" "4.22985076083931e-50" "3.15647320589307e-50"
## [5,] "0.285008742405142" "1.73754775003521e-83" "1.29662326806482e-83"
## [6,] "0.28500874228266" "1.00203957573045e-166" "7.47759495753465e-167"
print(Export_Summary_SNV(Input = Result_HLA1_SNV, Mut_Rank_th = 5, Wt_Rank_th = 5))
## Num_All_Alteration Num_Evaluated_Alteration
## 3 3
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 2 114
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 113 3
Result_HLA1_SNV_vep <- MainSNVClass1(input_vep_format_file = "./../data/sample_vcf.vep.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c1.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCpan_dir = "./../lib/netMHCpan-4.0/netMHCpan",
multiple_variants = FALSE)
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Uploaded_variation\tLocation\tAllele\tGene\tFeature\tFeature_type\tConsequence\tcDNA_position\tCDS_position\tProtein_position\tAmino_acids\tCodons\tExisting_variation\tExtra"
## [1] "Executing Transformation"
## [1] "HLAtype: A*02:01" "HLAtype: A*32:01" "HLAtype: B*15:17" "HLAtype: B*51:01"
## [5] "HLAtype: C*07:01" "HLAtype: C*15:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Please Manually Indicate depth_normal_column if you want to use."
## [1] "Set depth_normal_column as NA NA"
## [1] "Please Manually Indicate depth_tumor_column if you want to use."
## [1] "Set depth_tumor_column as NA NA"
## [1] "Set nm_id_column as 10 AAChange.refGene"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tGeneDetail.refGene\tExonicFunc.refGene\tAAChange.refGene"
## [1] "Start Analysis: Mutation 1"
## [1] "NM_001282584 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "NM_001282582 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "NM_032348 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "NM_001282585 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "NM_001282583 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 2"
## [1] "NM_023014 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 3"
## [1] "NM_ID NOT Macth, Skip: NM_001405693"
## [1] "NM_ID NOT Macth, Skip: NM_001405684"
## [1] "NM_ID NOT Macth, Skip: NM_001405683"
## [1] "NM_ID NOT Macth, Skip: NM_001405673"
## [1] "NM_ID NOT Macth, Skip: NM_001405695"
## [1] "NM_ID NOT Macth, Skip: NM_001405670"
## [1] "NM_ID NOT Macth, Skip: NM_001405675"
## [1] "NM_ID NOT Macth, Skip: NM_001405686"
## [1] "NM_ID NOT Macth, Skip: NM_001405671"
## [1] "NM_ID NOT Macth, Skip: NM_001405696"
## [1] "NM_ID NOT Macth, Skip: NM_001405687"
## [1] "NM_ID NOT Macth, Skip: NM_001405668"
## [1] "NM_ID NOT Macth, Skip: NM_001405678"
## [1] "NM_ID NOT Macth, Skip: NM_001405680"
## [1] "NM_ID NOT Macth, Skip: NM_001405692"
## [1] "NM_ID NOT Macth, Skip: NM_001405669"
## [1] "NM_ID NOT Macth, Skip: NM_001405674"
## [1] "NM_ID NOT Macth, Skip: NM_001405682"
## [1] "NM_ID NOT Macth, Skip: NM_001405699"
## [1] "NM_ID NOT Macth, Skip: NM_001405700"
## [1] "NM_ID NOT Macth, Skip: NM_001405679"
## [1] "NM_ID NOT Macth, Skip: NM_001405697"
## [1] "NM_ID NOT Macth, Skip: NM_001405698"
## [1] "NM_ID NOT Macth, Skip: NM_001405685"
## [1] "NM_ID NOT Macth, Skip: NM_001405676"
## [1] "NM_ID NOT Macth, Skip: NM_001405681"
## [1] "NM_ID NOT Macth, Skip: NM_001405667"
## [1] "NM_ID NOT Macth, Skip: NM_001405694"
## [1] "NM_ID NOT Macth, Skip: NM_001405672"
## [1] "NM_ID NOT Macth, Skip: NM_001405677"
## [1] "NM_017940 - Ref Matched to and NM_ID Attached Information"
## [1] "End Position Amino Acid is not X, Skip NM_017940"
## [1] -999
## [1] "NM_ID NOT Macth, Skip: NM_001405666"
## [1] "Start Analysis: Mutation 4"
## [1] "NM_ID NOT Macth, Skip: NM_001405693"
## [1] "NM_ID NOT Macth, Skip: NM_001405684"
## [1] "NM_ID NOT Macth, Skip: NM_001405683"
## [1] "NM_ID NOT Macth, Skip: NM_001405673"
## [1] "NM_ID NOT Macth, Skip: NM_001405695"
## [1] "NM_ID NOT Macth, Skip: NM_001405670"
## [1] "NM_ID NOT Macth, Skip: NM_001405675"
## [1] "NM_ID NOT Macth, Skip: NM_001405686"
## [1] "NM_ID NOT Macth, Skip: NM_001405671"
## [1] "NM_ID NOT Macth, Skip: NM_001405696"
## [1] "NM_ID NOT Macth, Skip: NM_001405687"
## [1] "NM_ID NOT Macth, Skip: NM_001405668"
## [1] "NM_ID NOT Macth, Skip: NM_001405678"
## [1] "NM_ID NOT Macth, Skip: NM_001405680"
## [1] "NM_ID NOT Macth, Skip: NM_001405692"
## [1] "NM_ID NOT Macth, Skip: NM_001405669"
## [1] "NM_ID NOT Macth, Skip: NM_001405674"
## [1] "NM_ID NOT Macth, Skip: NM_001405682"
## [1] "NM_ID NOT Macth, Skip: NM_001405699"
## [1] "NM_ID NOT Macth, Skip: NM_001405700"
## [1] "NM_ID NOT Macth, Skip: NM_001405679"
## [1] "NM_ID NOT Macth, Skip: NM_001405697"
## [1] "NM_ID NOT Macth, Skip: NM_001405698"
## [1] "NM_ID NOT Macth, Skip: NM_001405685"
## [1] "NM_ID NOT Macth, Skip: NM_001405676"
## [1] "NM_ID NOT Macth, Skip: NM_001405681"
## [1] "NM_ID NOT Macth, Skip: NM_001405667"
## [1] "NM_ID NOT Macth, Skip: NM_001405694"
## [1] "NM_ID NOT Macth, Skip: NM_001405672"
## [1] "NM_ID NOT Macth, Skip: NM_001405677"
## [1] "NM_017940 - Ref Matched to and NM_ID Attached Information"
## [1] "End Position Amino Acid is not X, Skip NM_017940"
## [1] -999
## [1] "NM_ID NOT Macth, Skip: NM_001405666"
## [1] "Start Analysis: Mutation 5"
## [1] "NM_001164586 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "NM_001367841 - Ref Matched to and NM_ID Attached Information"
## [1] "The Mutation is not between Exon Region, Skip NM_001367841"
## [1] "result.ID.SNV1/sample_vcf.vep.txt.annovar_format.txt.ID_SNV.peptide.txt.list.vcf"
## [1] "Did not find ./../lib/netMHCpan-4.0/netMHCpan"
Result_HLA1_vep_SNV <- CalculatePriorityScores(result = Result_HLA1_SNV_vep, useRNAvaf = FALSE)
print(head(Result_HLA1_vep_SNV))
## result P_I P_R P
print(Export_Summary_SNV(Input = Result_HLA1_vep_SNV, Mut_Rank_th = 5, Wt_Rank_th = 5))
## Num_All_Alteration Num_Evaluated_Alteration
## 0 0
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 0 0
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 0 0
To calculate the binding affinity of neoantigen candaites, which are generated from from SNVs, to HLA ClassII.
Result_HLA2_SNV <- MainSNVClass2(input_annovar_format_file = "./../data/sample_vcf.annovar.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c2.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCIIpan_dir = "./../lib/netMHCIIpan-4.3/netMHCIIpan",
depth_tumor_column = 12,
depth_normal_column = 14,
SNPs = "./../data/sample_vcf.snps.txt",
multiple_variants = TRUE)
## [1] "HLAtype: DPA1*01:03" "HLAtype: DPA1*02:01" "HLAtype: DPB1*02:01"
## [4] "HLAtype: DPB1*09:01" "HLAtype: DQA1*01:02" "HLAtype: DQA1*05:05"
## [7] "HLAtype: DQB1*03:01" "HLAtype: DQB1*06:04" "HLAtype: DRB1*11:04"
## [10] "HLAtype: DRB1*13:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Set depth_normal_column as 14 depth_normal"
## [1] "Set depth_tumor_column as 12 depth_tumor"
## [1] "Set nm_id_column as 10 AAChange.refGene"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tGeneDetail.refGene\tExonicFunc.refGene\tAAChange.refGene\tcytoBand\tdepth_tumor\tvariantNum_tumor\tdepth_normal"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
## [1] "Start Analysis: Mutation 1"
## [1] "NM_001358 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 2"
## [1] "NM_002048 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 3"
## [1] "NM_006205 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.txt.list.vcf"
## [1] "Executing netMHCpan to result.ID.SNV2"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10201 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.1.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10901 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.2.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10201 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.3.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10901 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.4.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10301 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.5.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10604 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.6.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10301 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.7.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10604 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.8.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a DRB1_1104 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.9.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a DRB1_1302 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.10.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DPA10103 -choose -chb DPB10201 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.1.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DPA10103 -choose -chb DPB10901 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.2.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DPA10201 -choose -chb DPB10201 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.3.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DPA10201 -choose -chb DPB10901 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.4.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DQA10102 -choose -chb DQB10301 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.5.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DQA10102 -choose -chb DQB10604 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.6.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DQA10505 -choose -chb DQB10301 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.7.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DQA10505 -choose -chb DQB10604 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.8.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a DRB1_1104 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.9.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a DRB1_1302 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.10.wtpeptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.1.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.10.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.2.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.3.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.4.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.5.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.6.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.7.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.8.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.9.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA2_SNV <- CalculatePriorityScores(result = Result_HLA2_SNV, useRNAvaf = FALSE)
print(head(Result_HLA2_SNV))
## HLA Pos Gene Evaluated_Mutant_Peptide Mut_EL Mut_Rank
## [1,] "DRB1_0101" "2" "0_DHX15" "TPEPERDYLEAAIRA" "0.000549" "55.59"
## [2,] "DRB1_0101" "3" "0_DHX15" "PEPERDYLEAAIRAV" "0.007817" "26.45"
## [3,] "DRB1_0101" "4" "0_DHX15" "EPERDYLEAAIRAVI" "0.036515" "14.73"
## [4,] "DRB1_0101" "5" "0_DHX15" "PERDYLEAAIRAVIQ" "0.113296" "8.52"
## [5,] "DRB1_0101" "6" "0_DHX15" "ERDYLEAAIRAVIQI" "0.093106" "9.46"
## [6,] "DRB1_0101" "7" "0_DHX15" "RDYLEAAIRAVIQIH" "0.012420" "22.51"
## Evaluated_Wt_Peptide Wt_EL Wt_Rank Chr NM_ID Change Ref Alt
## [1,] "TPEPERDYLEAAIRT" "0.000295" "63.70" "4" "NM_001358" "c.A1012G" "T" "C"
## [2,] "PEPERDYLEAAIRTV" "0.004001" "32.76" "4" "NM_001358" "c.A1012G" "T" "C"
## [3,] "EPERDYLEAAIRTVI" "0.027292" "16.63" "4" "NM_001358" "c.A1012G" "T" "C"
## [4,] "PERDYLEAAIRTVIQ" "0.082495" "10.06" "4" "NM_001358" "c.A1012G" "T" "C"
## [5,] "ERDYLEAAIRTVIQI" "0.077206" "10.41" "4" "NM_001358" "c.A1012G" "T" "C"
## [6,] "RDYLEAAIRTVIQIH" "0.011714" "22.96" "4" "NM_001358" "c.A1012G" "T" "C"
## Prob Mutation_Prob. Exon_Start Exon_End Mutation_Position Total_Depth
## [1,] "0" "0" "24529097" "24586177" "4_24556416" "294"
## [2,] "0" "0" "24529097" "24586177" "4_24556416" "294"
## [3,] "0" "0" "24529097" "24586177" "4_24556416" "294"
## [4,] "0" "0" "24529097" "24586177" "4_24556416" "294"
## [5,] "0" "0" "24529097" "24586177" "4_24556416" "294"
## [6,] "0" "0" "24529097" "24586177" "4_24556416" "294"
## Tumor_Depth Wt_Peptide
## [1,] "143" "YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL"
## [2,] "143" "YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL"
## [3,] "143" "YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL"
## [4,] "143" "YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL"
## [5,] "143" "YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL"
## [6,] "143" "YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA
## [1,] "YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL" "1.35204" "NA" "NA"
## [2,] "YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL" "1.35204" "NA" "NA"
## [3,] "YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL" "1.35204" "NA" "NA"
## [4,] "YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL" "1.35204" "NA" "NA"
## [5,] "YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL" "1.35204" "NA" "NA"
## [6,] "YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL" "1.35204" "NA" "NA"
## Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max
## [1,] "0.657624897959184" "NA" "NA" "NA"
## [2,] "0.657624897959184" "NA" "NA" "NA"
## [3,] "0.657624897959184" "NA" "NA" "NA"
## [4,] "0.657624897959184" "NA" "NA" "NA"
## [5,] "0.657624897959184" "NA" "NA" "NA"
## [6,] "0.657624897959184" "NA" "NA" "NA"
## P_I P_R P
## [1,] "0.28500874167929" "2.43602580240382e-117" "1.8178537752065e-117"
## [2,] "0.285008733251095" "4.60667843033526e-54" "3.43767613934292e-54"
## [3,] "0.285008720402792" "1.2973123034524e-28" "9.68103074329359e-29"
## [4,] "0.285008669168784" "3.96176033890512e-15" "2.95641408290313e-15"
## [5,] "0.285008704455587" "3.60333080928503e-17" "2.68894053113598e-17"
## [6,] "0.285008740581003" "1.65572875348136e-45" "1.23556686561528e-45"
print(Export_Summary_SNV(Input = Result_HLA2_SNV, Mut_Rank_th = 10, Wt_Rank_th = 10))
## Num_All_Alteration Num_Evaluated_Alteration
## 3 3
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 1 45
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 45 3
To calculate the binding affinity of neoantigen candaites, which are generated from from indels, to HLA ClassI. When using MHCflurry, [[1]] and [[2]] include the results of NetMHCpan and MHCflurry, respectively.
Result_HLA1_INDEL <- MainINDELClass1(input_annovar_format_file = "./../data/sample_vcf.annovar.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c1.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCpan_dir = "./../lib/netMHCpan-4.1/netMHCpan",
depth_tumor_column = 12,
depth_normal_column = 14,
SNPs = "./../data/sample_vcf.snps.txt",
multiple_variants = TRUE)
## [1] "HLAtype: A*02:01" "HLAtype: A*32:01" "HLAtype: B*15:17" "HLAtype: B*51:01"
## [5] "HLAtype: C*07:01" "HLAtype: C*15:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Set depth_normal_column as 14 depth_normal"
## [1] "Set depth_tumor_column as 12 depth_tumor"
## [1] "Set nm_id_column as 10 AAChange.refGene"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tGeneDetail.refGene\tExonicFunc.refGene\tAAChange.refGene\tcytoBand\tdepth_tumor\tvariantNum_tumor\tdepth_normal"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
## [1] "Start Analysis: Mutation 1"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 2"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 3"
## [1] "Peptide Successfully Generated!!"
## [1] "Peptide Successfully Generated!!"
## [1] "Peptide Successfully Generated!!"
## [1] "Peptide Successfully Generated!!"
## [1] "result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.txt.list.vcf"
## [1] "Executing netMHCpan to result.ID.INDEL1"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a HLA-A02:01 > result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.1.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a HLA-A32:01 > result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.2.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a HLA-B15:17 > result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.3.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a HLA-B51:01 > result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.4.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a HLA-C07:01 > result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.5.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a HLA-C15:02 > result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.6.peptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.1.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.2.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.3.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.4.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.5.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.6.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA1_INDEL_1 <- CalculatePriorityScores(result = Result_HLA1_INDEL, useRNAvaf = FALSE)
print(head(Result_HLA1_INDEL_1))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core
## [1,] "HLA-A*02:01" "1" "0_UGT2B28" "YHGIPMVGIPF"
## [2,] "HLA-A*02:01" "2" "0_UGT2B28" "HGIPMVGIPFV"
## [3,] "HLA-A*02:01" "3" "0_UGT2B28" "GIPMVGIPFVL"
## [4,] "HLA-A*02:01" "4" "0_UGT2B28" "IPMVGIPFVL"
## [5,] "HLA-A*02:01" "5" "0_UGT2B28" "PMVGIPFVLGS"
## [6,] "HLA-A*02:01" "6" "0_UGT2B28" "MVGIPFVLGST"
## Evaluated_Mutant_Peptide Mut_EL Mut_Rank Chr NM_ID
## [1,] "YHGIPMVGIPF" "0.0000510" "50.667" "4" "NM_053039"
## [2,] "HGIPMVGIPFV" "0.0034220" "10.843" "4" "NM_053039"
## [3,] "GIPMVGIPFVL" "0.0346280" "3.599" "4" "NM_053039"
## [4,] "IPMVGIPFVLG" "0.0006810" "20.759" "4" "NM_053039"
## [5,] "PMVGIPFVLGS" "0.0000390" "54.667" "4" "NM_053039"
## [6,] "MVGIPFVLGST" "0.0001620" "35.154" "4" "NM_053039"
## Change Ref Alt Prob Mutation_Prob. Exon_Start Exon_End
## [1,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [2,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [3,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [4,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [5,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [6,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## Mutation_Position Total_Depth Tumor_Depth Wt_Peptide
## [1,] "4_70156404" "84" "43" "YHGIPMVGIPLFWDQPDNIAHMKAKGA"
## [2,] "4_70156404" "84" "43" "YHGIPMVGIPLFWDQPDNIAHMKAKGA"
## [3,] "4_70156404" "84" "43" "YHGIPMVGIPLFWDQPDNIAHMKAKGA"
## [4,] "4_70156404" "84" "43" "YHGIPMVGIPLFWDQPDNIAHMKAKGA"
## [5,] "4_70156404" "84" "43" "YHGIPMVGIPLFWDQPDNIAHMKAKGA"
## [6,] "4_70156404" "84" "43" "YHGIPMVGIPLFWDQPDNIAHMKAKGA"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA
## [1,] "YHGIPMVGIPFVLGSTX" "0" "NA" "NA"
## [2,] "YHGIPMVGIPFVLGSTX" "0" "NA" "NA"
## [3,] "YHGIPMVGIPFVLGSTX" "0" "NA" "NA"
## [4,] "YHGIPMVGIPFVLGSTX" "0" "NA" "NA"
## [5,] "YHGIPMVGIPFVLGSTX" "0" "NA" "NA"
## [6,] "YHGIPMVGIPFVLGSTX" "0" "NA" "NA"
## Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max P_I P_R P
## [1,] "0" "NA" "NA" "NA" "0" "0" "0"
## [2,] "0" "NA" "NA" "NA" "0" "0" "0"
## [3,] "0" "NA" "NA" "NA" "0" "0" "0"
## [4,] "0" "NA" "NA" "NA" "0" "0" "0"
## [5,] "0" "NA" "NA" "NA" "0" "0" "0"
## [6,] "0" "NA" "NA" "NA" "0" "0" "0"
print(Export_Summary_IndelSV(Input = Result_HLA1_INDEL_1, Mut_Rank_th = 5))
## Num_All_Alteration Num_Evaluated_Alteration
## 3 3
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 3 184
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 184 53
print(Export_Summary_IndelSV_perFragments(Input = Result_HLA1_INDEL_1, Mut_Rank_th = 5))
## YHGIPMVGIPFVLGSTX-0_UGT2B28
## Num_Peptide_Per_Pep 24.000
## Num_Cond_Peptide_Per_Pep 24.000
## Num_Rest_Peptide_Per_Pep 10.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.417
## -logP 0.391
## RDELLAAIKKFHIKVATQX-1_COL12A1
## Num_Peptide_Per_Pep 32.000
## Num_Cond_Peptide_Per_Pep 32.000
## Num_Rest_Peptide_Per_Pep 7.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.219
## -logP 0.437
## ARDFLPSLKNRFWKPSILPIFMYKHCSVQFSVRHGDVQTKVHX-2_SLCO1C1
## Num_Peptide_Per_Pep 128.000
## Num_Cond_Peptide_Per_Pep 128.000
## Num_Rest_Peptide_Per_Pep 36.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.281
## -logP 0.989
To calculate the binding affinity of neoantigen candaites, which are generated from from indels, to HLA ClassII.
Result_HLA2_INDEL <- MainINDELClass2(input_annovar_format_file = "./../data/sample_vcf.annovar.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c2.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCIIpan_dir = "./../lib/netMHCIIpan-4.3/netMHCIIpan",
depth_tumor_column = 12,
depth_normal_column = 14,
SNPs = "./../data/sample_vcf.snps.txt",
multiple_variants = TRUE)
## [1] "HLAtype: DPA1*01:03" "HLAtype: DPA1*02:01" "HLAtype: DPB1*02:01"
## [4] "HLAtype: DPB1*09:01" "HLAtype: DQA1*01:02" "HLAtype: DQA1*05:05"
## [7] "HLAtype: DQB1*03:01" "HLAtype: DQB1*06:04" "HLAtype: DRB1*11:04"
## [10] "HLAtype: DRB1*13:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Set depth_normal_column as 14 depth_normal"
## [1] "Set depth_tumor_column as 12 depth_tumor"
## [1] "Set nm_id_column as 10 AAChange.refGene"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tGeneDetail.refGene\tExonicFunc.refGene\tAAChange.refGene\tcytoBand\tdepth_tumor\tvariantNum_tumor\tdepth_normal"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
## [1] "Start Analysis: Mutation 1"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 2"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 3"
## [1] "Peptide Successfully Generated!!"
## [1] "Peptide Successfully Generated!!"
## [1] "Peptide Successfully Generated!!"
## [1] "Peptide Successfully Generated!!"
## [1] "result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.txt.list.vcf"
## [1] "Executing netMHCpan to result.ID.INDEL2"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10201 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.1.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10901 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.2.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10201 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.3.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10901 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.4.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10301 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.5.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10604 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.6.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10301 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.7.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10604 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.8.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a DRB1_1104 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.9.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a DRB1_1302 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.10.peptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.1.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.10.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.2.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.3.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.4.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.5.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.6.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.7.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.8.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.9.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA2_INDEL <- CalculatePriorityScores(result = Result_HLA2_INDEL, useRNAvaf = FALSE)
print(head(Result_HLA2_INDEL))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core
## [1,] "DRB1_0101" "1" "0_UGT2B28" "YHGIPMVGI"
## [2,] "DRB1_0101" "2" "0_UGT2B28" "YHGIPMVGI"
## [3,] "DRB1_0101" "3" "0_UGT2B28" "YHGIPMVGI"
## [4,] "DRB1_0101" "4" "0_UGT2B28" "GIPMVGIPF"
## [5,] "DRB1_0101" "5" "0_UGT2B28" "MVGIPFVLG"
## [6,] "DRB1_0101" "6" "0_UGT2B28" "MVGIPFVLG"
## Evaluated_Mutant_Peptide Mut_EL Mut_Rank Chr NM_ID
## [1,] "YEAIYHGIPMVGIPF" "0.068310" "11.01" "4" "NM_053039"
## [2,] "EAIYHGIPMVGIPFV" "0.064542" "11.34" "4" "NM_053039"
## [3,] "AIYHGIPMVGIPFVL" "0.005254" "30.11" "4" "NM_053039"
## [4,] "IYHGIPMVGIPFVLG" "0.000447" "58.35" "4" "NM_053039"
## [5,] "YHGIPMVGIPFVLGS" "0.000776" "51.47" "4" "NM_053039"
## [6,] "HGIPMVGIPFVLGST" "0.001719" "41.82" "4" "NM_053039"
## Change Ref Alt Prob Mutation_Prob. Exon_Start Exon_End
## [1,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [2,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [3,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [4,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [5,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [6,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## Mutation_Position Total_Depth Tumor_Depth
## [1,] "4_70156404" "84" "43"
## [2,] "4_70156404" "84" "43"
## [3,] "4_70156404" "84" "43"
## [4,] "4_70156404" "84" "43"
## [5,] "4_70156404" "84" "43"
## [6,] "4_70156404" "84" "43"
## Wt_Peptide Mutant_Peptide Total_RNA
## [1,] "YEAIYHGIPMVGIPLFWDQPDNIAHMKAKGA" "YEAIYHGIPMVGIPFVLGSTX" "0"
## [2,] "YEAIYHGIPMVGIPLFWDQPDNIAHMKAKGA" "YEAIYHGIPMVGIPFVLGSTX" "0"
## [3,] "YEAIYHGIPMVGIPLFWDQPDNIAHMKAKGA" "YEAIYHGIPMVGIPFVLGSTX" "0"
## [4,] "YEAIYHGIPMVGIPLFWDQPDNIAHMKAKGA" "YEAIYHGIPMVGIPFVLGSTX" "0"
## [5,] "YEAIYHGIPMVGIPLFWDQPDNIAHMKAKGA" "YEAIYHGIPMVGIPFVLGSTX" "0"
## [6,] "YEAIYHGIPMVGIPLFWDQPDNIAHMKAKGA" "YEAIYHGIPMVGIPFVLGSTX" "0"
## Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio MutRatio_Min
## [1,] "NA" "NA" "0" "NA" "NA"
## [2,] "NA" "NA" "0" "NA" "NA"
## [3,] "NA" "NA" "0" "NA" "NA"
## [4,] "NA" "NA" "0" "NA" "NA"
## [5,] "NA" "NA" "0" "NA" "NA"
## [6,] "NA" "NA" "0" "NA" "NA"
## MutRatio_Max P_I P_R P
## [1,] "NA" "0" "0" "0"
## [2,] "NA" "0" "0" "0"
## [3,] "NA" "0" "0" "0"
## [4,] "NA" "0" "0" "0"
## [5,] "NA" "0" "0" "0"
## [6,] "NA" "0" "0" "0"
print(Export_Summary_IndelSV(Input = Result_HLA2_INDEL, , Mut_Rank_th = 10))
## Num_All_Alteration Num_Evaluated_Alteration
## 3 3
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 2 46
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 46 10
print(Export_Summary_IndelSV_perFragments(Input = Result_HLA2_INDEL, , Mut_Rank_th = 5))
## YEAIYHGIPMVGIPFVLGSTX-0_UGT2B28
## Num_Peptide_Per_Pep 6.000
## Num_Cond_Peptide_Per_Pep 6.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.483
## QYYQRDELLAAIKKFHIKVATQX-1_COL12A1
## Num_Peptide_Per_Pep 8.000
## Num_Cond_Peptide_Per_Pep 8.000
## Num_Rest_Peptide_Per_Pep 5.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.625
## -logP 0.529
## IMEMARDFLPSLKNRFWKPSILPIFMYKHCSVQFSVRHGDVQTKVHX-2_SLCO1C1
## Num_Peptide_Per_Pep 32.000
## Num_Cond_Peptide_Per_Pep 32.000
## Num_Rest_Peptide_Per_Pep 4.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.125
## -logP 1.081
To calculate the binding affinity of neoantigen candaites, which are generated from from SVs, to HLA ClassI.
Result_HLA1_SV <- MainSVFUSIONClass1(input_file = "./../data/sample_sv_bnd.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c1.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCpan_dir = "./../lib/netMHCpan-4.1/netMHCpan",
refdna_file = "./../lib/GRCh37.fa",
mutation_alt_bnd_column = 5,
gene_symbol_column = 7,
mate_id_column = 8)
## [1] "HLAtype: A*02:01" "HLAtype: A*32:01" "HLAtype: B*15:17" "HLAtype: B*51:01"
## [5] "HLAtype: C*07:01" "HLAtype: C*15:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Please Manually Indicate depth_normal_column if you want to use."
## [1] "Set depth_normal_column as NA NA"
## [1] "Please Manually Indicate depth_tumor_column if you want to use."
## [1] "Set depth_tumor_column as NA NA"
## [1] "Set nm_id_column as 0 "
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tmateID"
## [1] "Start Analysis: Mutation SVMERGE137"
## [1] "OK SVMERGE137"
## [1] "Start Analysis: Mutation SVMERGE15"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE15"
## [1] "Start Analysis: Mutation SVMERGE116"
## [1] "OK SVMERGE116"
## [1] "Start Analysis: Mutation SVMERGE3"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE3"
## [1] "Start Analysis: Mutation SVMERGE38"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE38"
## [1] "OK SVMERGE38"
## [1] "OK SVMERGE38"
## [1] "OK SVMERGE38"
## [1] "Start Analysis: Mutation SVMERGE195"
## [1] "OK SVMERGE195"
## [1] "OK SVMERGE195"
## [1] "Start Analysis: Mutation SVMERGE10"
## [1] "Start Analysis: Mutation SVMERGE272"
## [1] "OK SVMERGE272"
## [1] "Start Analysis: Mutation SVMERGE101"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE101"
## [1] "Start Analysis: Mutation SVMERGE40"
## [1] "OK SVMERGE40"
## [1] "Start Analysis: Mutation SVMERGE460"
## [1] "OK SVMERGE460"
## [1] "Start Analysis: Mutation SVMERGE133"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "OK SVMERGE133"
## [1] "Start Analysis: Mutation SVMERGE31"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE157"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE72"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE177"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE37"
## [1] "Non-Stop!!"
## [1] "Non-Stop!!"
## [1] "OK SVMERGE37"
## [1] "Start Analysis: Mutation SVMERGE206"
## [1] "OK SVMERGE206"
## [1] "Start Analysis: Mutation SVMERGE58"
## [1] "OK SVMERGE58"
## [1] "Start Analysis: Mutation SVMERGE210"
## [1] "OK SVMERGE210"
## [1] "Start Analysis: Mutation SVMERGE205"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.txt.list.vcf"
## [1] "Executing netMHCpan to result.ID.SV1"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a HLA-A02:01 > result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.1.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a HLA-A32:01 > result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.2.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a HLA-B15:17 > result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.3.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a HLA-B51:01 > result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.4.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a HLA-C07:01 > result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.5.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a HLA-C15:02 > result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.6.peptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.1.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.2.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.3.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.4.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.5.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.6.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA1_SV <- CalculatePriorityScores(result = Result_HLA1_SV, useRNAvaf = FALSE)
print(head(Result_HLA1_SV))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core
## [1,] "HLA-A*02:01" "1" "0_AAR2" "DYNSWEVGPKFRE"
## [2,] "HLA-A*02:01" "2" "0_AAR2" "YNSWEVGPKFREQ"
## [3,] "HLA-A*02:01" "3" "0_AAR2" "NSWEVGPKFREQL"
## [4,] "HLA-A*02:01" "4" "0_AAR2" "SWEVGPKFREQLK"
## [5,] "HLA-A*02:01" "5" "0_AAR2" "WEVGPKFREQLKL"
## [6,] "HLA-A*02:01" "6" "0_AAR2" "EVGPKFREQLKL"
## Evaluated_Mutant_Peptide Mut_EL Mut_Rank Chr NM_ID
## [1,] "DYNSWEVGPKFRE" "0.0000010" "95.000" "20" "NM_015511_NM_015906"
## [2,] "YNSWEVGPKFREQ" "0.0000080" "76.667" "20" "NM_015511_NM_015906"
## [3,] "NSWEVGPKFREQL" "0.0004280" "24.750" "20" "NM_015511_NM_015906"
## [4,] "SWEVGPKFREQLK" "0.0000030" "87.500" "20" "NM_015511_NM_015906"
## [5,] "WEVGPKFREQLKL" "0.0000430" "53.333" "20" "NM_015511_NM_015906"
## [6,] "EVGPKFREQLKLF" "0.0000060" "80.000" "20" "NM_015511_NM_015906"
## Change Ref Alt Prob Mutation_Prob.
## [1,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [2,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [3,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [4,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [5,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [6,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## Exon_Start Exon_End Mutation_Position Total_Depth Tumor_Depth
## [1,] "34824338" "34844863" "20_34827929" "0" "0"
## [2,] "34824338" "34844863" "20_34827929" "0" "0"
## [3,] "34824338" "34844863" "20_34827929" "0" "0"
## [4,] "34824338" "34844863" "20_34827929" "0" "0"
## [5,] "34824338" "34844863" "20_34827929" "0" "0"
## [6,] "34824338" "34844863" "20_34827929" "0" "0"
## Wt_Peptide
## [1,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [2,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [3,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [4,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [5,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [6,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA
## [1,] "DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE" "3.03498" "NA" "NA"
## [2,] "DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE" "3.03498" "NA" "NA"
## [3,] "DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE" "3.03498" "NA" "NA"
## [4,] "DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE" "3.03498" "NA" "NA"
## [5,] "DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE" "3.03498" "NA" "NA"
## [6,] "DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE" "3.03498" "NA" "NA"
## Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max
## [1,] "NaN" "NA" "NA" "NA"
## [2,] "NaN" "NA" "NA" "NA"
## [3,] "NaN" "NA" "NA" "NA"
## [4,] "NaN" "NA" "NA" "NA"
## [5,] "NaN" "NA" "NA" "NA"
## [6,] "NaN" "NA" "NA" "NA"
## P_I P_R P
## [1,] "0.994835363484567" "1.12475327099476e-202" "1.12475613722433e-202"
## [2,] "0.994835363426825" "7.25539311432306e-163" "7.25541160337557e-163"
## [3,] "0.994835359962294" "3.95361188289843e-50" "3.95362195796073e-50"
## [4,] "0.994835363468069" "2.17320320184772e-186" "2.17320873986164e-186"
## [5,] "0.994835363138115" "3.38686707516126e-112" "3.38687570597729e-112"
## [6,] "0.994835363443322" "4.19897614731469e-170" "4.19898684764329e-170"
print(Export_Summary_IndelSV(Result_HLA1_SV, , Mut_Rank_th = 5))
## Num_All_Alteration Num_Evaluated_Alteration
## 16 16
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 16 3183
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 3183 351
print(Export_Summary_IndelSV_perFragments(Result_HLA1_SV, , Mut_Rank_th = 5))
## DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE-0_AAR2
## Num_Peptide_Per_Pep 57.000
## Num_Cond_Peptide_Per_Pep 57.000
## Num_Rest_Peptide_Per_Pep 5.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.088
## -logP 0.782
## GDPHELRNIFLQLSAVQEAQLKRLEVTRPRVLGSREQGQVPRMARQPPPPWVHAAFLLCLLSLGG-1_SLC25A12
## Num_Peptide_Per_Pep 237.000
## Num_Cond_Peptide_Per_Pep 237.000
## Num_Rest_Peptide_Per_Pep 31.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.131
## -logP 1.496
## TMAEKRQLFIEMLYRLX-2_DTNB
## Num_Peptide_Per_Pep 24.000
## Num_Cond_Peptide_Per_Pep 24.000
## Num_Rest_Peptide_Per_Pep 7.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.292
## -logP 0.391
## TDWLSDCCFHPSERCRCTLYGHTDSVNSIEFFP-3_SPAG16
## Num_Peptide_Per_Pep 51.000
## Num_Cond_Peptide_Per_Pep 51.000
## Num_Rest_Peptide_Per_Pep 2.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.039
## -logP 0.759
## MKSCKRNLSTTTGSSERX-4_TMCC1
## Num_Peptide_Per_Pep 45.000
## Num_Cond_Peptide_Per_Pep 45.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.414
## ACLPGEEGTAERSCKRNLSTTTGSSERX-5_TMCC1
## Num_Peptide_Per_Pep 90.000
## Num_Cond_Peptide_Per_Pep 90.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.644
## VQRFSLRRQLSKSCKRNLSTTTGSSERX-6_TMCC1
## Num_Peptide_Per_Pep 90.000
## Num_Cond_Peptide_Per_Pep 90.000
## Num_Rest_Peptide_Per_Pep 3.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.033
## -logP 0.644
## QRKGSYCWDFEESCKRNLSTTTGSSERX-7_TMCC1
## Num_Peptide_Per_Pep 90.000
## Num_Cond_Peptide_Per_Pep 90.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.644
## IRPKPFVIPGRSRTLECKQQKIILLRREMKETX-8_PDLIM3
## Num_Peptide_Per_Pep 120.000
## Num_Cond_Peptide_Per_Pep 120.000
## Num_Rest_Peptide_Per_Pep 12.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.100
## -logP 0.759
## GQLRGLIPSSPQKTLECKQQKIILLRREMKETX-9_PDLIM3
## Num_Peptide_Per_Pep 120.000
## Num_Cond_Peptide_Per_Pep 120.000
## Num_Rest_Peptide_Per_Pep 19.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.158
## -logP 0.759
## GDQYIVDMANTKRTLLWTRPMTVILGKPFCVMPKQQKTAHIGFLQHIPRLSPKPCLPKLNLMMRKQRMSQNGKNVKFEESHLRAVCMSGRGMGQVWVFFLCSX-10_WDR70
## Num_Peptide_Per_Pep 540.00
## Num_Cond_Peptide_Per_Pep 540.00
## Num_Rest_Peptide_Per_Pep 81.00
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.15
## -logP 2.37
## LCPASRALEEKKGHELLGGPSLGAPRPGSQERTGENTAACQDHRFWAGQTAGCGRERIPCRRRQSAYQVDGIGINFTQNLYPPEX-11_EGFR
## Num_Peptide_Per_Pep 432.000
## Num_Cond_Peptide_Per_Pep 432.000
## Num_Rest_Peptide_Per_Pep 24.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.056
## -logP 1.956
## LTPMPEGLSQQQDMLKNTSKGHPDRLPLQMALT-12_ARHGEF10
## Num_Peptide_Per_Pep 51.000
## Num_Cond_Peptide_Per_Pep 51.000
## Num_Rest_Peptide_Per_Pep 3.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.059
## -logP 0.759
## PGVQGKKVRKPSPTTSASSSSWTSAGTSWPAGRRTGTATSGTATTTSVWPGCGTRMWSTQWSSVPRSRSCCSRPATTPPSKPGAPHAPCASSRHLAHGLAPSSPGLPARGAEVCWVHWSHRDPLRTSPGSVAFSRAGEVEMLIAVTPX-13_NOTCH1
## Num_Peptide_Per_Pep 810.000
## Num_Cond_Peptide_Per_Pep 810.000
## Num_Rest_Peptide_Per_Pep 97.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.120
## -logP 3.405
## SRGRGNNNRKGREVTPL-14_UBAP2
## Num_Peptide_Per_Pep 30.000
## Num_Cond_Peptide_Per_Pep 30.000
## Num_Rest_Peptide_Per_Pep 1.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.033
## -logP 0.391
## IPSSQLAAKLLHMLTMRMLSKSATGRWX-15_RASGRP2
## Num_Peptide_Per_Pep 90.000
## Num_Cond_Peptide_Per_Pep 90.000
## Num_Rest_Peptide_Per_Pep 20.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.222
## -logP 0.644
## RKSPPEKKLRRYPPGQGATIGVDFMIKTVEINGE-16_GAB2
## Num_Peptide_Per_Pep 57.000
## Num_Cond_Peptide_Per_Pep 57.000
## Num_Rest_Peptide_Per_Pep 11.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.193
## -logP 0.782
## MSVIVLPQPDEVLNLVQSYVTLRVPLYVSYVFH-17_MTRF1
## Num_Peptide_Per_Pep 51.000
## Num_Cond_Peptide_Per_Pep 51.000
## Num_Rest_Peptide_Per_Pep 12.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.235
## -logP 0.759
## LWKCLRKPVLNDRNLQLHTDKGSFLKEKNKKLKKK-18_EVI2B
## Num_Peptide_Per_Pep 63.000
## Num_Cond_Peptide_Per_Pep 63.000
## Num_Rest_Peptide_Per_Pep 8.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.127
## -logP 0.805
## RTFLQSTDPGDTGGVFEGSTLCPSDPAFSRTDDPX-19_IKZF3
## Num_Peptide_Per_Pep 132.000
## Num_Cond_Peptide_Per_Pep 132.000
## Num_Rest_Peptide_Per_Pep 9.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.068
## -logP 0.805
## RDALTGHLRTHSGGVFEGSTLCPSDPAFSRTDDPX-20_IKZF3
## Num_Peptide_Per_Pep 132.000
## Num_Cond_Peptide_Per_Pep 132.000
## Num_Rest_Peptide_Per_Pep 10.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.076
## -logP 0.805
## GEGPANEDEDIGGGVFEGSTLCPSDPAFSRTDDPX-21_IKZF3
## Num_Peptide_Per_Pep 132.000
## Num_Cond_Peptide_Per_Pep 132.000
## Num_Rest_Peptide_Per_Pep 5.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.038
## -logP 0.805
## NVLMVHKRSHTGGVFEGSTLCPSDPAFSRTDDPX-22_IKZF3
## Num_Peptide_Per_Pep 126.000
## Num_Cond_Peptide_Per_Pep 126.000
## Num_Rest_Peptide_Per_Pep 10.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.079
## -logP 0.782
## FNVLMVHKRSHTGGVFEGSTLCPSDPAFSRTDDPX-23_IKZF3
## Num_Peptide_Per_Pep 132.000
## Num_Cond_Peptide_Per_Pep 132.000
## Num_Rest_Peptide_Per_Pep 10.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.076
## -logP 0.805
To calculate the binding affinity of neoantigen candaites, which are generated from from SVs, to HLA ClassII.
Result_HLA2_SV <- MainSVFUSIONClass2(input_file = "./../data/sample_sv_bnd.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c2.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCIIpan_dir = "./../lib/netMHCIIpan-4.3/netMHCIIpan",
refdna_file = "./../lib/GRCh37.fa",
mutation_alt_bnd_column = 5,
gene_symbol_column = 7,
mate_id_column = 8)
## [1] "HLAtype: DPA1*01:03" "HLAtype: DPA1*02:01" "HLAtype: DPB1*02:01"
## [4] "HLAtype: DPB1*09:01" "HLAtype: DQA1*01:02" "HLAtype: DQA1*05:05"
## [7] "HLAtype: DQB1*03:01" "HLAtype: DQB1*06:04" "HLAtype: DRB1*11:04"
## [10] "HLAtype: DRB1*13:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Please Manually Indicate depth_normal_column if you want to use."
## [1] "Set depth_normal_column as NA NA"
## [1] "Please Manually Indicate depth_tumor_column if you want to use."
## [1] "Set depth_tumor_column as NA NA"
## [1] "Set nm_id_column as 0 "
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tmateID"
## [1] "Start Analysis: Mutation SVMERGE137"
## [1] "OK SVMERGE137"
## [1] "Start Analysis: Mutation SVMERGE15"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE15"
## [1] "Start Analysis: Mutation SVMERGE116"
## [1] "OK SVMERGE116"
## [1] "Start Analysis: Mutation SVMERGE3"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE3"
## [1] "Start Analysis: Mutation SVMERGE38"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE38"
## [1] "OK SVMERGE38"
## [1] "OK SVMERGE38"
## [1] "OK SVMERGE38"
## [1] "Start Analysis: Mutation SVMERGE195"
## [1] "OK SVMERGE195"
## [1] "OK SVMERGE195"
## [1] "Start Analysis: Mutation SVMERGE10"
## [1] "Start Analysis: Mutation SVMERGE272"
## [1] "OK SVMERGE272"
## [1] "Start Analysis: Mutation SVMERGE101"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE101"
## [1] "Start Analysis: Mutation SVMERGE40"
## [1] "OK SVMERGE40"
## [1] "Start Analysis: Mutation SVMERGE460"
## [1] "OK SVMERGE460"
## [1] "Start Analysis: Mutation SVMERGE133"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "OK SVMERGE133"
## [1] "Start Analysis: Mutation SVMERGE31"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE157"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE72"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE177"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE37"
## [1] "Non-Stop!!"
## [1] "Non-Stop!!"
## [1] "OK SVMERGE37"
## [1] "Start Analysis: Mutation SVMERGE206"
## [1] "OK SVMERGE206"
## [1] "Start Analysis: Mutation SVMERGE58"
## [1] "OK SVMERGE58"
## [1] "Start Analysis: Mutation SVMERGE210"
## [1] "OK SVMERGE210"
## [1] "Start Analysis: Mutation SVMERGE205"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.txt.list.vcf"
## [1] "Executing netMHCpan to result.ID.SV2"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10201 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.1.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10901 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.2.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10201 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.3.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10901 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.4.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10301 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.5.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10604 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.6.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10301 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.7.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10604 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.8.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a DRB1_1104 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.9.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a DRB1_1302 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.10.peptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.1.peptide.txt"
## [1] "4.16666666666667 perc. fin"
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## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.10.peptide.txt"
## [1] "4.16666666666667 perc. fin"
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## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.2.peptide.txt"
## [1] "4.16666666666667 perc. fin"
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## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.3.peptide.txt"
## [1] "4.16666666666667 perc. fin"
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## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.4.peptide.txt"
## [1] "4.16666666666667 perc. fin"
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## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.5.peptide.txt"
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## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.6.peptide.txt"
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## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.7.peptide.txt"
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## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.8.peptide.txt"
## [1] "4.16666666666667 perc. fin"
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## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.9.peptide.txt"
## [1] "4.16666666666667 perc. fin"
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## [1] "54.1666666666667 perc. fin"
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## [1] "Successfully Finished."
Result_HLA2_SV <- CalculatePriorityScores(result = Result_HLA2_SV, useRNAvaf = FALSE)
print(head(Result_HLA2_SV))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core
## [1,] "DRB1_0101" "1" "0_AAR2" "YNSWEVGPK"
## [2,] "DRB1_0101" "2" "0_AAR2" "YNSWEVGPK"
## [3,] "DRB1_0101" "3" "0_AAR2" "YNSWEVGPK"
## [4,] "DRB1_0101" "4" "0_AAR2" "WEVGPKFRE"
## [5,] "DRB1_0101" "5" "0_AAR2" "WEVGPKFRE"
## [6,] "DRB1_0101" "6" "0_AAR2" "VGPKFREQL"
## Evaluated_Mutant_Peptide Mut_EL Mut_Rank Chr NM_ID
## [1,] "GIDYNSWEVGPKFRE" "0.002971" "35.75" "20" "NM_015511_NM_015906"
## [2,] "IDYNSWEVGPKFREQ" "0.000624" "54.09" "20" "NM_015511_NM_015906"
## [3,] "DYNSWEVGPKFREQL" "0.000203" "68.45" "20" "NM_015511_NM_015906"
## [4,] "YNSWEVGPKFREQLK" "0.000105" "76.22" "20" "NM_015511_NM_015906"
## [5,] "NSWEVGPKFREQLKL" "0.000042" "85.71" "20" "NM_015511_NM_015906"
## [6,] "SWEVGPKFREQLKLF" "0.000009" "95.50" "20" "NM_015511_NM_015906"
## Change Ref Alt Prob Mutation_Prob.
## [1,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [2,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [3,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [4,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [5,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [6,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## Exon_Start Exon_End Mutation_Position Total_Depth Tumor_Depth
## [1,] "34824338" "34844863" "20_34827929" "0" "0"
## [2,] "34824338" "34844863" "20_34827929" "0" "0"
## [3,] "34824338" "34844863" "20_34827929" "0" "0"
## [4,] "34824338" "34844863" "20_34827929" "0" "0"
## [5,] "34824338" "34844863" "20_34827929" "0" "0"
## [6,] "34824338" "34844863" "20_34827929" "0" "0"
## Wt_Peptide
## [1,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [2,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [3,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [4,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [5,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [6,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio
## [1,] "GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK" "3.03498" "NA"
## [2,] "GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK" "3.03498" "NA"
## [3,] "GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK" "3.03498" "NA"
## [4,] "GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK" "3.03498" "NA"
## [5,] "GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK" "3.03498" "NA"
## [6,] "GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK" "3.03498" "NA"
## Tumor_RNA Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max
## [1,] "NA" "NaN" "NA" "NA" "NA"
## [2,] "NA" "NaN" "NA" "NA" "NA"
## [3,] "NA" "NaN" "NA" "NA" "NA"
## [4,] "NA" "NaN" "NA" "NA" "NA"
## [5,] "NA" "NaN" "NA" "NA" "NA"
## [6,] "NA" "NaN" "NA" "NA" "NA"
## P_I P_R P
## [1,] "0.994835338984919" "5.13804056470373e-74" "5.13805365806756e-74"
## [2,] "0.994835358345505" "7.69118996528602e-114" "7.69120956488771e-114"
## [3,] "0.994835361818295" "5.05416874225877e-145" "5.05418162189048e-145"
## [4,] "0.994835362626685" "6.78124000735739e-162" "6.78125728811676e-162"
## [5,] "0.994835363146364" "1.67508152720577e-182" "1.67508579584702e-182"
## [6,] "0.994835363418576" "9.23253707018305e-204" "9.23256059762808e-204"
print(Export_Summary_IndelSV(Result_HLA2_SV, Mut_Rank_th = 5))
## Num_All_Alteration Num_Evaluated_Alteration
## 16 16
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 8 588
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 588 30
print(Export_Summary_IndelSV_perFragments(Result_HLA2_SV, Mut_Rank_th = 5))
## GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK-0_AAR2
## Num_Peptide_Per_Pep 14.000
## Num_Cond_Peptide_Per_Pep 14.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.874
## KRGDPHELRNIFLQLSAVQEAQLKRLEVTRPRVLGSREQGQVPRMARQPPPPWVHAAFLLCLLSLGGAI-1_SLC25A12
## Num_Peptide_Per_Pep 44.000
## Num_Cond_Peptide_Per_Pep 44.000
## Num_Rest_Peptide_Per_Pep 3.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.068
## -logP 1.588
## RKTMAEKRQLFIEMLYRLX-2_DTNB
## Num_Peptide_Per_Pep 4.000
## Num_Cond_Peptide_Per_Pep 4.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.437
## GHTDWLSDCCFHPSERCRCTLYGHTDSVNSIEFFPFS-3_SPAG16
## Num_Peptide_Per_Pep 13.000
## Num_Cond_Peptide_Per_Pep 13.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.851
## MKSCKRNLSTTTGSSERX-4_TMCC1
## Num_Peptide_Per_Pep 3.000
## Num_Cond_Peptide_Per_Pep 3.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.414
## AAACLPGEEGTAERSCKRNLSTTTGSSERX-5_TMCC1
## Num_Peptide_Per_Pep 15.00
## Num_Cond_Peptide_Per_Pep 15.00
## Num_Rest_Peptide_Per_Pep 0.00
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.00
## -logP 0.69
## MVQRFSLRRQLSKSCKRNLSTTTGSSERX-6_TMCC1
## Num_Peptide_Per_Pep 14.000
## Num_Cond_Peptide_Per_Pep 14.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.667
## PMQRKGSYCWDFEESCKRNLSTTTGSSERX-7_TMCC1
## Num_Peptide_Per_Pep 15.00
## Num_Cond_Peptide_Per_Pep 15.00
## Num_Rest_Peptide_Per_Pep 0.00
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.00
## -logP 0.69
## HNIRPKPFVIPGRSRTLECKQQKIILLRREMKETX-8_PDLIM3
## Num_Peptide_Per_Pep 20.000
## Num_Cond_Peptide_Per_Pep 20.000
## Num_Rest_Peptide_Per_Pep 2.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.100
## -logP 0.805
## LHGQLRGLIPSSPQKTLECKQQKIILLRREMKETX-9_PDLIM3
## Num_Peptide_Per_Pep 20.000
## Num_Cond_Peptide_Per_Pep 20.000
## Num_Rest_Peptide_Per_Pep 2.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.100
## -logP 0.805
## IKGDQYIVDMANTKRTLLWTRPMTVILGKPFCVMPKQQKTAHIGFLQHIPRLSPKPCLPKLNLMMRKQRMSQNGKNVKFEESHLRAVCMSGRGMGQVWVFFLCSX-10_WDR70
## Num_Peptide_Per_Pep 90.000
## Num_Cond_Peptide_Per_Pep 90.000
## Num_Rest_Peptide_Per_Pep 16.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.178
## -logP 2.416
## AALCPASRALEEKKGHELLGGPSLGAPRPGSQERTGENTAACQDHRFWAGQTAGCGRERIPCRRRQSAYQVDGIGINFTQNLYPPEX-11_EGFR
## Num_Peptide_Per_Pep 72.000
## Num_Cond_Peptide_Per_Pep 72.000
## Num_Rest_Peptide_Per_Pep 1.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.014
## -logP 2.002
## AILTPMPEGLSQQQDMLKNTSKGHPDRLPLQMALTEL-12_ARHGEF10
## Num_Peptide_Per_Pep 13.000
## Num_Cond_Peptide_Per_Pep 13.000
## Num_Rest_Peptide_Per_Pep 1.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.077
## -logP 0.851
## LKPGVQGKKVRKPSPTTSASSSSWTSAGTSWPAGRRTGTATSGTATTTSVWPGCGTRMWSTQWSSVPRSRSCCSRPATTPPSKPGAPHAPCASSRHLAHGLAPSSPGLPARGAEVCWVHWSHRDPLRTSPGSVAFSRAGEVEMLIAVTPX-13_NOTCH1
## Num_Peptide_Per_Pep 135.000
## Num_Cond_Peptide_Per_Pep 135.000
## Num_Rest_Peptide_Per_Pep 1.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.007
## -logP 3.451
## ESSRGRGNNNRKGREVTPL-14_UBAP2
## Num_Peptide_Per_Pep 5.000
## Num_Cond_Peptide_Per_Pep 5.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.437
## WYIPSSQLAAKLLHMLTMRMLSKSATGRWX-15_RASGRP2
## Num_Peptide_Per_Pep 15.00
## Num_Cond_Peptide_Per_Pep 15.00
## Num_Rest_Peptide_Per_Pep 3.00
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.20
## -logP 0.69
## WLRKSPPEKKLRRYPPGQGATIGVDFMIKTVEINGEKV-16_GAB2
## Num_Peptide_Per_Pep 14.000
## Num_Cond_Peptide_Per_Pep 14.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.874
## GTMSVIVLPQPDEVLNLVQSYVTLRVPLYVSYVFHSP-17_MTRF1
## Num_Peptide_Per_Pep 13.000
## Num_Cond_Peptide_Per_Pep 13.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.851
## IVLWKCLRKPVLNDRNLQLHTDKGSFLKEKNKKLKKKNK-18_EVI2B
## Num_Peptide_Per_Pep 15.000
## Num_Cond_Peptide_Per_Pep 15.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.897
## RCRTFLQSTDPGDTGGVFEGSTLCPSDPAFSRTDDPX-19_IKZF3
## Num_Peptide_Per_Pep 22.000
## Num_Cond_Peptide_Per_Pep 22.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.851
## QRRDALTGHLRTHSGGVFEGSTLCPSDPAFSRTDDPX-20_IKZF3
## Num_Peptide_Per_Pep 22.000
## Num_Cond_Peptide_Per_Pep 22.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.851
## DSGEGPANEDEDIGGGVFEGSTLCPSDPAFSRTDDPX-21_IKZF3
## Num_Peptide_Per_Pep 22.000
## Num_Cond_Peptide_Per_Pep 22.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.851
## SFNVLMVHKRSHTGGVFEGSTLCPSDPAFSRTDDPX-22_IKZF3
## Num_Peptide_Per_Pep 21.000
## Num_Cond_Peptide_Per_Pep 21.000
## Num_Rest_Peptide_Per_Pep 2.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.095
## -logP 0.828
## ISFNVLMVHKRSHTGGVFEGSTLCPSDPAFSRTDDPX-23_IKZF3
## Num_Peptide_Per_Pep 22.000
## Num_Cond_Peptide_Per_Pep 22.000
## Num_Rest_Peptide_Per_Pep 3.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.136
## -logP 0.851
To calculate the binding affinity of neoantigen candaites, which are directly generated from RNA sequences, to HLA ClassI. The peptides included in the original genes ("NM_003998", "NM_001165412") are removed from the results.
Result_HLA1_Seq <- MainSeqFragmentClass1(input_sequence = "atggcagaagatgatccatatttgggaaggcctgaaaaaatgtttcatttggatccttctttgactcatacaatatttaatc",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c1.txt",
hmdir = getwd(),
job_id = "NO_job_id",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
netMHCpan_dir = "./../lib/netMHCpan-4.1/netMHCpan",
reference_nm_id = c("NM_003998", "NM_001165412"))
## [1] "Sequence: atggcagaagatgatccatatttgggaaggcctgaaaaaatgtttcatttggatccttctttgactcatacaatatttaatc"
## [1] "HLAtype: A*02:01" "HLAtype: A*32:01" "HLAtype: B*15:17" "HLAtype: B*51:01"
## [5] "HLAtype: C*07:01" "HLAtype: C*15:02"
## [1] "refFLAT: ./../lib/refFlat.grch37.txt"
## [1] "refMrna: ./../lib/refMrna.grch37.fa"
## [1] "Wt-NM_ID: NM_003998" "Wt-NM_ID: NM_001165412"
## [1] "Wt-Gene Symbol: NA"
## [1] "Start Position of Reading Frame is: 1"
## [1] "Peptide Successfully Generated!!"
## [1] "Executing netMHCpan to result.NO_job_id.SeqFragment1"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.peptide.fasta -a HLA-A02:01 > result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.1.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.peptide.fasta -a HLA-A32:01 > result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.2.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.peptide.fasta -a HLA-B15:17 > result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.3.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.peptide.fasta -a HLA-B51:01 > result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.4.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.peptide.fasta -a HLA-C07:01 > result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.5.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.peptide.fasta -a HLA-C15:02 > result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.6.peptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.1.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.2.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.3.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.4.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.5.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.6.peptide.txt"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA1_Seq <- CalculatePriorityScores(result = Result_HLA1_Seq, useRNAvaf = FALSE)
## Warning in CalculatePriorityScores(result = Result_HLA1_Seq, useRNAvaf =
## FALSE): NAs introduced by coercion
print(head(Result_HLA1_Seq))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core
## [1,] "HLA-A*02:01" "1" "0_atggcagaag" "MAEDDPYLGRPEK"
## [2,] "HLA-A*02:01" "2" "0_atggcagaag" "AEDDPYLGRPEKM"
## [3,] "HLA-A*02:01" "3" "0_atggcagaag" "EDDPYLGRPEKMF"
## [4,] "HLA-A*02:01" "4" "0_atggcagaag" "DDPYLGRPEKMFH"
## [5,] "HLA-A*02:01" "5" "0_atggcagaag" "YLGRPEKMFHL"
## [6,] "HLA-A*02:01" "6" "0_atggcagaag" "YLGRPEKMFHL"
## Evaluated_Mutant_Peptide Mut_EL Mut_Rank Chr NM_ID ReadingFrame
## [1,] "MAEDDPYLGRPEK" "0.0000280" "59.545" "0" "" "1"
## [2,] "AEDDPYLGRPEKM" "0.0001790" "33.938" "0" "" "1"
## [3,] "EDDPYLGRPEKMF" "0.0000050" "82.500" "0" "" "1"
## [4,] "DDPYLGRPEKMFH" "0.0000010" "95.000" "0" "" "1"
## [5,] "DPYLGRPEKMFHL" "0.0001750" "34.214" "0" "" "1"
## [6,] "PYLGRPEKMFHLD" "0.0000040" "85.000" "0" "" "1"
## SequenceNumber Chrs NM_IDs GeneIDs
## [1,] "1" "chr4;chr4" "NM_003998;NM_001165412" "NFKB1;NFKB1"
## [2,] "1" "chr4;chr4" "NM_003998;NM_001165412" "NFKB1;NFKB1"
## [3,] "1" "chr4;chr4" "NM_003998;NM_001165412" "NFKB1;NFKB1"
## [4,] "1" "chr4;chr4" "NM_003998;NM_001165412" "NFKB1;NFKB1"
## [5,] "1" "chr4;chr4" "NM_003998;NM_001165412" "NFKB1;NFKB1"
## [6,] "1" "chr4;chr4" "NM_003998;NM_001165412" "NFKB1;NFKB1"
## Exon_Starts Exon_Ends GroupID NumOfPeptides
## [1,] "103422515;103422515" "103538459;103538459" "0_1" "27"
## [2,] "103422515;103422515" "103538459;103538459" "0_1" "27"
## [3,] "103422515;103422515" "103538459;103538459" "0_1" "27"
## [4,] "103422515;103422515" "103538459;103538459" "0_1" "27"
## [5,] "103422515;103422515" "103538459;103538459" "0_1" "27"
## [6,] "103422515;103422515" "103538459;103538459" "0_1" "27"
## NumOfStops
## [1,] "0"
## [2,] "0"
## [3,] "0"
## [4,] "0"
## [5,] "0"
## [6,] "0"
## Wt_Peptide
## [1,] "MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [2,] "MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [3,] "MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [4,] "MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [5,] "MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [6,] "MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA
## [1,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [2,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [3,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [4,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [5,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [6,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max P_I P_R P
## [1,] "NA" "NA" "NA" "NA" NA NA NA
## [2,] "NA" "NA" "NA" "NA" NA NA NA
## [3,] "NA" "NA" "NA" "NA" NA NA NA
## [4,] "NA" "NA" "NA" "NA" NA NA NA
## [5,] "NA" "NA" "NA" "NA" NA NA NA
## [6,] "NA" "NA" "NA" "NA" NA NA NA
print(Export_Summary_Fragments(Result_HLA1_Seq, Mut_Rank_th = 5))
## [[1]]
## atggcagaag
## Num_Peptide_Per_Grp 63.000
## Num_Cond_Peptide_Per_Grp 63.000
## Num_Rest_Peptide_Per_Grp 15.000
## Num_Rest_Peptide_Per_Grp / Num_Cond_Peptide_Per_Grp 0.238
## -logP 0.621
##
## [[2]]
##
## Num_Peptide_Per_NM 63.000
## Num_Cond_Peptide_Per_NM 63.000
## Num_Rest_Peptide_Per_NM 15.000
## Num_Rest_Peptide_Per_NM / Num_Cond_Peptide_Per_NM 0.238
## -logP 0.621
##
## [[3]]
## MAEDDPYLGRPEKMFHLDPSLTHTIFN-0_atggcagaag-0_1
## Num_Peptide_Per_Pep 63.000
## Num_Cond_Peptide_Per_Pep 63.000
## Num_Rest_Peptide_Per_Pep 15.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.238
## -logP 0.621
To calculate the binding affinity of neoantigen candaites, which are directly generated from RNA sequences, to HLA ClassII. The peptides included in the riginal genes ("NFKB1", "BCL3") are removed from the results.
Result_HLA2_Seq <- MainSeqFragmentClass2(input_sequence = "atggcagaagatgatccatatttgggaaggcctgaaaaaatgtttcatttggatccttctttgactcatacaatatttaatc",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c2.txt",
hmdir = getwd(),
job_id = "NO_job_id",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
netMHCIIpan_dir = "./../lib/netMHCIIpan-4.3/netMHCIIpan",
reference_gene_symbol = c("NFKB1", "BCL3"))
## [1] "Sequence: atggcagaagatgatccatatttgggaaggcctgaaaaaatgtttcatttggatccttctttgactcatacaatatttaatc"
## [1] "HLAtype: DPA1*01:03" "HLAtype: DPA1*02:01" "HLAtype: DPB1*02:01"
## [4] "HLAtype: DPB1*09:01" "HLAtype: DQA1*01:02" "HLAtype: DQA1*05:05"
## [7] "HLAtype: DQB1*03:01" "HLAtype: DQB1*06:04" "HLAtype: DRB1*11:04"
## [10] "HLAtype: DRB1*13:02"
## [1] "refFLAT: ./../lib/refFlat.grch37.txt"
## [1] "refMrna: ./../lib/refMrna.grch37.fa"
## [1] "Wt-NM_ID: NA"
## [1] "Wt-Gene Symbol: NFKB1" "Wt-Gene Symbol: BCL3"
## [1] "Start Position of Reading Frame is: 1"
## [1] "Peptide Successfully Generated!!"
## [1] "Executing netMHCpan to result.NO_job_id.SeqFragment2"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10201 > result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.1.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10901 > result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.2.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10201 > result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.3.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10901 > result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.4.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10301 > result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.5.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10604 > result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.6.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10301 > result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.7.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10604 > result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.8.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -a DRB1_1104 > result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.9.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -a DRB1_1302 > result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.10.peptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.1.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.10.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.2.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.3.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.4.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.9.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.5.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.6.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.7.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.8.peptide.txt"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA2_Seq <- CalculatePriorityScores(result = Result_HLA2_Seq, useRNAvaf = FALSE)
## Warning in CalculatePriorityScores(result = Result_HLA2_Seq, useRNAvaf =
## FALSE): NAs introduced by coercion
print(head(Result_HLA2_Seq))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core
## [1,] "DRB1_0101" "1" "0_atggcagaag" "PYLGRPEKM"
## [2,] "DRB1_0101" "2" "0_atggcagaag" "YLGRPEKMF"
## [3,] "DRB1_0101" "3" "0_atggcagaag" "YLGRPEKMF"
## [4,] "DRB1_0101" "4" "0_atggcagaag" "YLGRPEKMF"
## [5,] "DRB1_0101" "5" "0_atggcagaag" "YLGRPEKMF"
## [6,] "DRB1_0101" "6" "0_atggcagaag" "GRPEKMFHL"
## Evaluated_Mutant_Peptide Mut_EL Mut_Rank Chr NM_ID ReadingFrame
## [1,] "MAEDDPYLGRPEKMF" "0.000116" "74.92" "0" "" "1"
## [2,] "AEDDPYLGRPEKMFH" "0.000639" "53.83" "0" "" "1"
## [3,] "EDDPYLGRPEKMFHL" "0.000790" "51.22" "0" "" "1"
## [4,] "DDPYLGRPEKMFHLD" "0.001267" "45.36" "0" "" "1"
## [5,] "DPYLGRPEKMFHLDP" "0.000216" "67.70" "0" "" "1"
## [6,] "PYLGRPEKMFHLDPS" "0.000048" "84.48" "0" "" "1"
## SequenceNumber Chrs
## [1,] "1" "chr19;chr4;chr4;chr4;chr4;chr4;chr4;chr4"
## [2,] "1" "chr19;chr4;chr4;chr4;chr4;chr4;chr4;chr4"
## [3,] "1" "chr19;chr4;chr4;chr4;chr4;chr4;chr4;chr4"
## [4,] "1" "chr19;chr4;chr4;chr4;chr4;chr4;chr4;chr4"
## [5,] "1" "chr19;chr4;chr4;chr4;chr4;chr4;chr4;chr4"
## [6,] "1" "chr19;chr4;chr4;chr4;chr4;chr4;chr4;chr4"
## NM_IDs
## [1,] "NM_005178;NM_001319226;NM_003998;NM_001165412;NM_001382626;NM_001382627;NM_001382628;NM_001382625"
## [2,] "NM_005178;NM_001319226;NM_003998;NM_001165412;NM_001382626;NM_001382627;NM_001382628;NM_001382625"
## [3,] "NM_005178;NM_001319226;NM_003998;NM_001165412;NM_001382626;NM_001382627;NM_001382628;NM_001382625"
## [4,] "NM_005178;NM_001319226;NM_003998;NM_001165412;NM_001382626;NM_001382627;NM_001382628;NM_001382625"
## [5,] "NM_005178;NM_001319226;NM_003998;NM_001165412;NM_001382626;NM_001382627;NM_001382628;NM_001382625"
## [6,] "NM_005178;NM_001319226;NM_003998;NM_001165412;NM_001382626;NM_001382627;NM_001382628;NM_001382625"
## GeneIDs
## [1,] "BCL3;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1"
## [2,] "BCL3;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1"
## [3,] "BCL3;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1"
## [4,] "BCL3;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1"
## [5,] "BCL3;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1"
## [6,] "BCL3;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1"
## Exon_Starts
## [1,] "45251964;103423090;103422515;103422515;103422515;103422515;103422515;103423090"
## [2,] "45251964;103423090;103422515;103422515;103422515;103422515;103422515;103423090"
## [3,] "45251964;103423090;103422515;103422515;103422515;103422515;103422515;103423090"
## [4,] "45251964;103423090;103422515;103422515;103422515;103422515;103422515;103423090"
## [5,] "45251964;103423090;103422515;103422515;103422515;103422515;103422515;103423090"
## [6,] "45251964;103423090;103422515;103422515;103422515;103422515;103422515;103423090"
## Exon_Ends
## [1,] "45263301;103538459;103538459;103538459;103538459;103538459;103538459;103538459"
## [2,] "45263301;103538459;103538459;103538459;103538459;103538459;103538459;103538459"
## [3,] "45263301;103538459;103538459;103538459;103538459;103538459;103538459;103538459"
## [4,] "45263301;103538459;103538459;103538459;103538459;103538459;103538459;103538459"
## [5,] "45263301;103538459;103538459;103538459;103538459;103538459;103538459;103538459"
## [6,] "45263301;103538459;103538459;103538459;103538459;103538459;103538459;103538459"
## GroupID NumOfPeptides NumOfStops
## [1,] "0_1" "27" "0"
## [2,] "0_1" "27" "0"
## [3,] "0_1" "27" "0"
## [4,] "0_1" "27" "0"
## [5,] "0_1" "27" "0"
## [6,] "0_1" "27" "0"
## Wt_Peptide
## [1,] "MPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [2,] "MPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [3,] "MPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [4,] "MPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [5,] "MPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [6,] "MPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA
## [1,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [2,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [3,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [4,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [5,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [6,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max P_I P_R P
## [1,] "NA" "NA" "NA" "NA" NA NA NA
## [2,] "NA" "NA" "NA" "NA" NA NA NA
## [3,] "NA" "NA" "NA" "NA" NA NA NA
## [4,] "NA" "NA" "NA" "NA" NA NA NA
## [5,] "NA" "NA" "NA" "NA" NA NA NA
## [6,] "NA" "NA" "NA" "NA" NA NA NA
print(Export_Summary_Fragments(Result_HLA2_Seq, Mut_Rank_th = 5))
## [[1]]
## atggcagaag
## Num_Peptide_Per_Grp 13.000
## Num_Cond_Peptide_Per_Grp 13.000
## Num_Rest_Peptide_Per_Grp 3.000
## Num_Rest_Peptide_Per_Grp / Num_Cond_Peptide_Per_Grp 0.231
## -logP 0.621
##
## [[2]]
##
## Num_Peptide_Per_NM 13.000
## Num_Cond_Peptide_Per_NM 13.000
## Num_Rest_Peptide_Per_NM 3.000
## Num_Rest_Peptide_Per_NM / Num_Cond_Peptide_Per_NM 0.231
## -logP 0.621
##
## [[3]]
## MAEDDPYLGRPEKMFHLDPSLTHTIFN-0_atggcagaag-0_1
## Num_Peptide_Per_Pep 13.000
## Num_Cond_Peptide_Per_Pep 13.000
## Num_Rest_Peptide_Per_Pep 3.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.231
## -logP 0.621
hase62/Neoantimon documentation built on July 8, 2024, 11:48 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
title: "SampleCodeForNeoantimon" author: "T. Hasegawa" date: "2024/6/12" output: pdf_document: default html_document: default
```{=html}
## Data Preparation and Sample Codes for Analysis
``` r
#install.packages('devtools');
library(devtools);
## Loading required package: usethis
install_github('hase62/Neoantimon');
## Skipping install of 'Neoantimon' from a github remote, the SHA1 (2ed545f8) has not changed since last install.
## Use `force = TRUE` to force installation
library(Neoantimon);
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("biomaRt")
## Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 (2024-04-24)
## Warning: package(s) not installed when version(s) same as or greater than current; use
## `force = TRUE` to re-install: 'biomaRt'
library(biomaRt)
To calculate the binding affinity of neoantigen candaites, which are generated from from SNVs, to HLA ClassI. When using MHCflurry, [[1]] and [[2]] include the results of NetMHCpan and MHCflurry, respectively.
Result_HLA1_SNV <- MainSNVClass1(input_annovar_format_file = "./../data/sample_vcf.annovar.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c1.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCpan_dir = "./../lib/netMHCpan-4.1/netMHCpan",
depth_tumor_column = 12,
depth_normal_column = 14,
SNPs = "./../data/sample_vcf.snps.txt",
multiple_variants = TRUE)
## [1] "HLAtype: A*02:01" "HLAtype: A*32:01" "HLAtype: B*15:17" "HLAtype: B*51:01"
## [5] "HLAtype: C*07:01" "HLAtype: C*15:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Set depth_normal_column as 14 depth_normal"
## [1] "Set depth_tumor_column as 12 depth_tumor"
## [1] "Set nm_id_column as 10 AAChange.refGene"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tGeneDetail.refGene\tExonicFunc.refGene\tAAChange.refGene\tcytoBand\tdepth_tumor\tvariantNum_tumor\tdepth_normal"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
## [1] "Start Analysis: Mutation 1"
## [1] "NM_001358 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 2"
## [1] "NM_002048 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 3"
## [1] "NM_006205 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.txt.list.vcf"
## [1] "Executing netMHCpan to result.ID.SNV1"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a HLA-A02:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.1.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a HLA-A32:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.2.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a HLA-B15:17 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.3.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a HLA-B51:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.4.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a HLA-C07:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.5.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a HLA-C15:02 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.6.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a HLA-A02:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.1.wtpeptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a HLA-A32:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.2.wtpeptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a HLA-B15:17 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.3.wtpeptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a HLA-B51:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.4.wtpeptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a HLA-C07:01 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.5.wtpeptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a HLA-C15:02 > result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.6.wtpeptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.1.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.2.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.3.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.4.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.5.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV1/sample_vcf.annovar.txt.ID_SNV.HLACLASS1.6.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA1_SNV <- CalculatePriorityScores(result = Result_HLA1_SNV, useRNAvaf = FALSE)
print(head(Result_HLA1_SNV))
## HLA Pos Gene Evaluated_Mutant_Peptide Mut_EL Mut_Rank
## [1,] "HLA-A*02:01" "2" "0_DHX15" "ERDYLEAAIRA" "0.0001110" "39.889"
## [2,] "HLA-A*02:01" "3" "0_DHX15" "RDYLEAAIRAV" "0.0093530" "6.946"
## [3,] "HLA-A*02:01" "4" "0_DHX15" "DYLEAAIRAVI" "0.0003140" "27.742"
## [4,] "HLA-A*02:01" "5" "0_DHX15" "YLEAAIRAVIQ" "0.0004340" "24.625"
## [5,] "HLA-A*02:01" "6" "0_DHX15" "LEAAIRAVIQI" "0.0001100" "40.000"
## [6,] "HLA-A*02:01" "7" "0_DHX15" "EAAIRAVIQIH" "0.0000070" "78.333"
## Evaluated_Wt_Peptide Wt_EL Wt_Rank Chr NM_ID Change Ref
## [1,] "ERDYLEAAIRT" "0.0000310" "58.182" "4" "NM_001358" "c.A1012G" "T"
## [2,] "RDYLEAAIRTV" "0.0192400" "4.851" "4" "NM_001358" "c.A1012G" "T"
## [3,] "DYLEAAIRTVI" "0.0003800" "25.878" "4" "NM_001358" "c.A1012G" "T"
## [4,] "YLEAAIRTVIQ" "0.0009320" "18.339" "4" "NM_001358" "c.A1012G" "T"
## [5,] "LEAAIRTVIQI" "0.0001630" "35.077" "4" "NM_001358" "c.A1012G" "T"
## [6,] "EAAIRTVIQIH" "0.0000080" "76.667" "4" "NM_001358" "c.A1012G" "T"
## Alt Prob Mutation_Prob. Exon_Start Exon_End Mutation_Position
## [1,] "C" "0" "0" "24529097" "24586177" "4_24556416"
## [2,] "C" "0" "0" "24529097" "24586177" "4_24556416"
## [3,] "C" "0" "0" "24529097" "24586177" "4_24556416"
## [4,] "C" "0" "0" "24529097" "24586177" "4_24556416"
## [5,] "C" "0" "0" "24529097" "24586177" "4_24556416"
## [6,] "C" "0" "0" "24529097" "24586177" "4_24556416"
## Total_Depth Tumor_Depth Wt_Peptide
## [1,] "294" "143" "PERDYLEAAIRTVIQIHMCEEEE"
## [2,] "294" "143" "PERDYLEAAIRTVIQIHMCEEEE"
## [3,] "294" "143" "PERDYLEAAIRTVIQIHMCEEEE"
## [4,] "294" "143" "PERDYLEAAIRTVIQIHMCEEEE"
## [5,] "294" "143" "PERDYLEAAIRTVIQIHMCEEEE"
## [6,] "294" "143" "PERDYLEAAIRTVIQIHMCEEEE"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA
## [1,] "PERDYLEAAIRAVIQIHMCEEEE" "1.35204" "NA" "NA"
## [2,] "PERDYLEAAIRAVIQIHMCEEEE" "1.35204" "NA" "NA"
## [3,] "PERDYLEAAIRAVIQIHMCEEEE" "1.35204" "NA" "NA"
## [4,] "PERDYLEAAIRAVIQIHMCEEEE" "1.35204" "NA" "NA"
## [5,] "PERDYLEAAIRAVIQIHMCEEEE" "1.35204" "NA" "NA"
## [6,] "PERDYLEAAIRAVIQIHMCEEEE" "1.35204" "NA" "NA"
## Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max
## [1,] "0.657624897959184" "NA" "NA" "NA"
## [2,] "0.657624897959184" "NA" "NA" "NA"
## [3,] "0.657624897959184" "NA" "NA" "NA"
## [4,] "0.657624897959184" "NA" "NA" "NA"
## [5,] "0.657624897959184" "NA" "NA" "NA"
## [6,] "0.657624897959184" "NA" "NA" "NA"
## P_I P_R P
## [1,] "0.28500874209118" "3.02670563878825e-83" "2.25864121245377e-83"
## [2,] "0.285008765600042" "1.03701641904894e-11" "7.73860527445574e-12"
## [3,] "0.285008742435297" "7.20851064695389e-57" "5.37926087656814e-57"
## [4,] "0.28500874345477" "4.22985076083931e-50" "3.15647320589307e-50"
## [5,] "0.285008742405142" "1.73754775003521e-83" "1.29662326806482e-83"
## [6,] "0.28500874228266" "1.00203957573045e-166" "7.47759495753465e-167"
print(Export_Summary_SNV(Input = Result_HLA1_SNV, Mut_Rank_th = 5, Wt_Rank_th = 5))
## Num_All_Alteration Num_Evaluated_Alteration
## 3 3
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 2 114
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 113 3
Result_HLA1_SNV_vep <- MainSNVClass1(input_vep_format_file = "./../data/sample_vcf.vep.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c1.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCpan_dir = "./../lib/netMHCpan-4.0/netMHCpan",
multiple_variants = FALSE)
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Uploaded_variation\tLocation\tAllele\tGene\tFeature\tFeature_type\tConsequence\tcDNA_position\tCDS_position\tProtein_position\tAmino_acids\tCodons\tExisting_variation\tExtra"
## [1] "Executing Transformation"
## [1] "HLAtype: A*02:01" "HLAtype: A*32:01" "HLAtype: B*15:17" "HLAtype: B*51:01"
## [5] "HLAtype: C*07:01" "HLAtype: C*15:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Please Manually Indicate depth_normal_column if you want to use."
## [1] "Set depth_normal_column as NA NA"
## [1] "Please Manually Indicate depth_tumor_column if you want to use."
## [1] "Set depth_tumor_column as NA NA"
## [1] "Set nm_id_column as 10 AAChange.refGene"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tGeneDetail.refGene\tExonicFunc.refGene\tAAChange.refGene"
## [1] "Start Analysis: Mutation 1"
## [1] "NM_001282584 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "NM_001282582 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "NM_032348 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "NM_001282585 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "NM_001282583 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 2"
## [1] "NM_023014 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 3"
## [1] "NM_ID NOT Macth, Skip: NM_001405693"
## [1] "NM_ID NOT Macth, Skip: NM_001405684"
## [1] "NM_ID NOT Macth, Skip: NM_001405683"
## [1] "NM_ID NOT Macth, Skip: NM_001405673"
## [1] "NM_ID NOT Macth, Skip: NM_001405695"
## [1] "NM_ID NOT Macth, Skip: NM_001405670"
## [1] "NM_ID NOT Macth, Skip: NM_001405675"
## [1] "NM_ID NOT Macth, Skip: NM_001405686"
## [1] "NM_ID NOT Macth, Skip: NM_001405671"
## [1] "NM_ID NOT Macth, Skip: NM_001405696"
## [1] "NM_ID NOT Macth, Skip: NM_001405687"
## [1] "NM_ID NOT Macth, Skip: NM_001405668"
## [1] "NM_ID NOT Macth, Skip: NM_001405678"
## [1] "NM_ID NOT Macth, Skip: NM_001405680"
## [1] "NM_ID NOT Macth, Skip: NM_001405692"
## [1] "NM_ID NOT Macth, Skip: NM_001405669"
## [1] "NM_ID NOT Macth, Skip: NM_001405674"
## [1] "NM_ID NOT Macth, Skip: NM_001405682"
## [1] "NM_ID NOT Macth, Skip: NM_001405699"
## [1] "NM_ID NOT Macth, Skip: NM_001405700"
## [1] "NM_ID NOT Macth, Skip: NM_001405679"
## [1] "NM_ID NOT Macth, Skip: NM_001405697"
## [1] "NM_ID NOT Macth, Skip: NM_001405698"
## [1] "NM_ID NOT Macth, Skip: NM_001405685"
## [1] "NM_ID NOT Macth, Skip: NM_001405676"
## [1] "NM_ID NOT Macth, Skip: NM_001405681"
## [1] "NM_ID NOT Macth, Skip: NM_001405667"
## [1] "NM_ID NOT Macth, Skip: NM_001405694"
## [1] "NM_ID NOT Macth, Skip: NM_001405672"
## [1] "NM_ID NOT Macth, Skip: NM_001405677"
## [1] "NM_017940 - Ref Matched to and NM_ID Attached Information"
## [1] "End Position Amino Acid is not X, Skip NM_017940"
## [1] -999
## [1] "NM_ID NOT Macth, Skip: NM_001405666"
## [1] "Start Analysis: Mutation 4"
## [1] "NM_ID NOT Macth, Skip: NM_001405693"
## [1] "NM_ID NOT Macth, Skip: NM_001405684"
## [1] "NM_ID NOT Macth, Skip: NM_001405683"
## [1] "NM_ID NOT Macth, Skip: NM_001405673"
## [1] "NM_ID NOT Macth, Skip: NM_001405695"
## [1] "NM_ID NOT Macth, Skip: NM_001405670"
## [1] "NM_ID NOT Macth, Skip: NM_001405675"
## [1] "NM_ID NOT Macth, Skip: NM_001405686"
## [1] "NM_ID NOT Macth, Skip: NM_001405671"
## [1] "NM_ID NOT Macth, Skip: NM_001405696"
## [1] "NM_ID NOT Macth, Skip: NM_001405687"
## [1] "NM_ID NOT Macth, Skip: NM_001405668"
## [1] "NM_ID NOT Macth, Skip: NM_001405678"
## [1] "NM_ID NOT Macth, Skip: NM_001405680"
## [1] "NM_ID NOT Macth, Skip: NM_001405692"
## [1] "NM_ID NOT Macth, Skip: NM_001405669"
## [1] "NM_ID NOT Macth, Skip: NM_001405674"
## [1] "NM_ID NOT Macth, Skip: NM_001405682"
## [1] "NM_ID NOT Macth, Skip: NM_001405699"
## [1] "NM_ID NOT Macth, Skip: NM_001405700"
## [1] "NM_ID NOT Macth, Skip: NM_001405679"
## [1] "NM_ID NOT Macth, Skip: NM_001405697"
## [1] "NM_ID NOT Macth, Skip: NM_001405698"
## [1] "NM_ID NOT Macth, Skip: NM_001405685"
## [1] "NM_ID NOT Macth, Skip: NM_001405676"
## [1] "NM_ID NOT Macth, Skip: NM_001405681"
## [1] "NM_ID NOT Macth, Skip: NM_001405667"
## [1] "NM_ID NOT Macth, Skip: NM_001405694"
## [1] "NM_ID NOT Macth, Skip: NM_001405672"
## [1] "NM_ID NOT Macth, Skip: NM_001405677"
## [1] "NM_017940 - Ref Matched to and NM_ID Attached Information"
## [1] "End Position Amino Acid is not X, Skip NM_017940"
## [1] -999
## [1] "NM_ID NOT Macth, Skip: NM_001405666"
## [1] "Start Analysis: Mutation 5"
## [1] "NM_001164586 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "NM_001367841 - Ref Matched to and NM_ID Attached Information"
## [1] "The Mutation is not between Exon Region, Skip NM_001367841"
## [1] "result.ID.SNV1/sample_vcf.vep.txt.annovar_format.txt.ID_SNV.peptide.txt.list.vcf"
## [1] "Did not find ./../lib/netMHCpan-4.0/netMHCpan"
Result_HLA1_vep_SNV <- CalculatePriorityScores(result = Result_HLA1_SNV_vep, useRNAvaf = FALSE)
print(head(Result_HLA1_vep_SNV))
## result P_I P_R P
print(Export_Summary_SNV(Input = Result_HLA1_vep_SNV, Mut_Rank_th = 5, Wt_Rank_th = 5))
## Num_All_Alteration Num_Evaluated_Alteration
## 0 0
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 0 0
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 0 0
To calculate the binding affinity of neoantigen candaites, which are generated from from SNVs, to HLA ClassII.
Result_HLA2_SNV <- MainSNVClass2(input_annovar_format_file = "./../data/sample_vcf.annovar.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c2.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCIIpan_dir = "./../lib/netMHCIIpan-4.3/netMHCIIpan",
depth_tumor_column = 12,
depth_normal_column = 14,
SNPs = "./../data/sample_vcf.snps.txt",
multiple_variants = TRUE)
## [1] "HLAtype: DPA1*01:03" "HLAtype: DPA1*02:01" "HLAtype: DPB1*02:01"
## [4] "HLAtype: DPB1*09:01" "HLAtype: DQA1*01:02" "HLAtype: DQA1*05:05"
## [7] "HLAtype: DQB1*03:01" "HLAtype: DQB1*06:04" "HLAtype: DRB1*11:04"
## [10] "HLAtype: DRB1*13:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Set depth_normal_column as 14 depth_normal"
## [1] "Set depth_tumor_column as 12 depth_tumor"
## [1] "Set nm_id_column as 10 AAChange.refGene"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tGeneDetail.refGene\tExonicFunc.refGene\tAAChange.refGene\tcytoBand\tdepth_tumor\tvariantNum_tumor\tdepth_normal"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
## [1] "Start Analysis: Mutation 1"
## [1] "NM_001358 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 2"
## [1] "NM_002048 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 3"
## [1] "NM_006205 - Ref Matched to and NM_ID Attached Information"
## [1] "Peptide Successfully Generated!!"
## [1] "result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.txt.list.vcf"
## [1] "Executing netMHCpan to result.ID.SNV2"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10201 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.1.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10901 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.2.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10201 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.3.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10901 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.4.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10301 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.5.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10604 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.6.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10301 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.7.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10604 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.8.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a DRB1_1104 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.9.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.peptide.fasta -a DRB1_1302 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.10.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DPA10103 -choose -chb DPB10201 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.1.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DPA10103 -choose -chb DPB10901 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.2.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DPA10201 -choose -chb DPB10201 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.3.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DPA10201 -choose -chb DPB10901 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.4.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DQA10102 -choose -chb DQB10301 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.5.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DQA10102 -choose -chb DQB10604 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.6.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DQA10505 -choose -chb DQB10301 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.7.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -choose -cha DQA10505 -choose -chb DQB10604 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.8.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a DRB1_1104 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.9.wtpeptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.wtpeptide.fasta -a DRB1_1302 > result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.10.wtpeptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.1.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.10.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.2.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.3.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.4.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.5.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.6.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.7.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.8.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SNV2/sample_vcf.annovar.txt.ID_SNV.HLACLASS2.9.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA2_SNV <- CalculatePriorityScores(result = Result_HLA2_SNV, useRNAvaf = FALSE)
print(head(Result_HLA2_SNV))
## HLA Pos Gene Evaluated_Mutant_Peptide Mut_EL Mut_Rank
## [1,] "DRB1_0101" "2" "0_DHX15" "TPEPERDYLEAAIRA" "0.000549" "55.59"
## [2,] "DRB1_0101" "3" "0_DHX15" "PEPERDYLEAAIRAV" "0.007817" "26.45"
## [3,] "DRB1_0101" "4" "0_DHX15" "EPERDYLEAAIRAVI" "0.036515" "14.73"
## [4,] "DRB1_0101" "5" "0_DHX15" "PERDYLEAAIRAVIQ" "0.113296" "8.52"
## [5,] "DRB1_0101" "6" "0_DHX15" "ERDYLEAAIRAVIQI" "0.093106" "9.46"
## [6,] "DRB1_0101" "7" "0_DHX15" "RDYLEAAIRAVIQIH" "0.012420" "22.51"
## Evaluated_Wt_Peptide Wt_EL Wt_Rank Chr NM_ID Change Ref Alt
## [1,] "TPEPERDYLEAAIRT" "0.000295" "63.70" "4" "NM_001358" "c.A1012G" "T" "C"
## [2,] "PEPERDYLEAAIRTV" "0.004001" "32.76" "4" "NM_001358" "c.A1012G" "T" "C"
## [3,] "EPERDYLEAAIRTVI" "0.027292" "16.63" "4" "NM_001358" "c.A1012G" "T" "C"
## [4,] "PERDYLEAAIRTVIQ" "0.082495" "10.06" "4" "NM_001358" "c.A1012G" "T" "C"
## [5,] "ERDYLEAAIRTVIQI" "0.077206" "10.41" "4" "NM_001358" "c.A1012G" "T" "C"
## [6,] "RDYLEAAIRTVIQIH" "0.011714" "22.96" "4" "NM_001358" "c.A1012G" "T" "C"
## Prob Mutation_Prob. Exon_Start Exon_End Mutation_Position Total_Depth
## [1,] "0" "0" "24529097" "24586177" "4_24556416" "294"
## [2,] "0" "0" "24529097" "24586177" "4_24556416" "294"
## [3,] "0" "0" "24529097" "24586177" "4_24556416" "294"
## [4,] "0" "0" "24529097" "24586177" "4_24556416" "294"
## [5,] "0" "0" "24529097" "24586177" "4_24556416" "294"
## [6,] "0" "0" "24529097" "24586177" "4_24556416" "294"
## Tumor_Depth Wt_Peptide
## [1,] "143" "YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL"
## [2,] "143" "YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL"
## [3,] "143" "YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL"
## [4,] "143" "YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL"
## [5,] "143" "YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL"
## [6,] "143" "YTPEPERDYLEAAIRTVIQIHMCEEEEGDLL"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA
## [1,] "YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL" "1.35204" "NA" "NA"
## [2,] "YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL" "1.35204" "NA" "NA"
## [3,] "YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL" "1.35204" "NA" "NA"
## [4,] "YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL" "1.35204" "NA" "NA"
## [5,] "YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL" "1.35204" "NA" "NA"
## [6,] "YTPEPERDYLEAAIRAVIQIHMCEEEEGDLL" "1.35204" "NA" "NA"
## Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max
## [1,] "0.657624897959184" "NA" "NA" "NA"
## [2,] "0.657624897959184" "NA" "NA" "NA"
## [3,] "0.657624897959184" "NA" "NA" "NA"
## [4,] "0.657624897959184" "NA" "NA" "NA"
## [5,] "0.657624897959184" "NA" "NA" "NA"
## [6,] "0.657624897959184" "NA" "NA" "NA"
## P_I P_R P
## [1,] "0.28500874167929" "2.43602580240382e-117" "1.8178537752065e-117"
## [2,] "0.285008733251095" "4.60667843033526e-54" "3.43767613934292e-54"
## [3,] "0.285008720402792" "1.2973123034524e-28" "9.68103074329359e-29"
## [4,] "0.285008669168784" "3.96176033890512e-15" "2.95641408290313e-15"
## [5,] "0.285008704455587" "3.60333080928503e-17" "2.68894053113598e-17"
## [6,] "0.285008740581003" "1.65572875348136e-45" "1.23556686561528e-45"
print(Export_Summary_SNV(Input = Result_HLA2_SNV, Mut_Rank_th = 10, Wt_Rank_th = 10))
## Num_All_Alteration Num_Evaluated_Alteration
## 3 3
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 1 45
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 45 3
To calculate the binding affinity of neoantigen candaites, which are generated from from indels, to HLA ClassI. When using MHCflurry, [[1]] and [[2]] include the results of NetMHCpan and MHCflurry, respectively.
Result_HLA1_INDEL <- MainINDELClass1(input_annovar_format_file = "./../data/sample_vcf.annovar.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c1.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCpan_dir = "./../lib/netMHCpan-4.1/netMHCpan",
depth_tumor_column = 12,
depth_normal_column = 14,
SNPs = "./../data/sample_vcf.snps.txt",
multiple_variants = TRUE)
## [1] "HLAtype: A*02:01" "HLAtype: A*32:01" "HLAtype: B*15:17" "HLAtype: B*51:01"
## [5] "HLAtype: C*07:01" "HLAtype: C*15:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Set depth_normal_column as 14 depth_normal"
## [1] "Set depth_tumor_column as 12 depth_tumor"
## [1] "Set nm_id_column as 10 AAChange.refGene"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tGeneDetail.refGene\tExonicFunc.refGene\tAAChange.refGene\tcytoBand\tdepth_tumor\tvariantNum_tumor\tdepth_normal"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
## [1] "Start Analysis: Mutation 1"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 2"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 3"
## [1] "Peptide Successfully Generated!!"
## [1] "Peptide Successfully Generated!!"
## [1] "Peptide Successfully Generated!!"
## [1] "Peptide Successfully Generated!!"
## [1] "result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.txt.list.vcf"
## [1] "Executing netMHCpan to result.ID.INDEL1"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a HLA-A02:01 > result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.1.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a HLA-A32:01 > result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.2.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a HLA-B15:17 > result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.3.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a HLA-B51:01 > result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.4.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a HLA-C07:01 > result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.5.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11 -f result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a HLA-C15:02 > result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.6.peptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.1.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.2.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.3.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.4.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.5.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL1/sample_vcf.annovar.txt.ID_INDEL.HLACLASS1.6.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA1_INDEL_1 <- CalculatePriorityScores(result = Result_HLA1_INDEL, useRNAvaf = FALSE)
print(head(Result_HLA1_INDEL_1))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core
## [1,] "HLA-A*02:01" "1" "0_UGT2B28" "YHGIPMVGIPF"
## [2,] "HLA-A*02:01" "2" "0_UGT2B28" "HGIPMVGIPFV"
## [3,] "HLA-A*02:01" "3" "0_UGT2B28" "GIPMVGIPFVL"
## [4,] "HLA-A*02:01" "4" "0_UGT2B28" "IPMVGIPFVL"
## [5,] "HLA-A*02:01" "5" "0_UGT2B28" "PMVGIPFVLGS"
## [6,] "HLA-A*02:01" "6" "0_UGT2B28" "MVGIPFVLGST"
## Evaluated_Mutant_Peptide Mut_EL Mut_Rank Chr NM_ID
## [1,] "YHGIPMVGIPF" "0.0000510" "50.667" "4" "NM_053039"
## [2,] "HGIPMVGIPFV" "0.0034220" "10.843" "4" "NM_053039"
## [3,] "GIPMVGIPFVL" "0.0346280" "3.599" "4" "NM_053039"
## [4,] "IPMVGIPFVLG" "0.0006810" "20.759" "4" "NM_053039"
## [5,] "PMVGIPFVLGS" "0.0000390" "54.667" "4" "NM_053039"
## [6,] "MVGIPFVLGST" "0.0001620" "35.154" "4" "NM_053039"
## Change Ref Alt Prob Mutation_Prob. Exon_Start Exon_End
## [1,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [2,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [3,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [4,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [5,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [6,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## Mutation_Position Total_Depth Tumor_Depth Wt_Peptide
## [1,] "4_70156404" "84" "43" "YHGIPMVGIPLFWDQPDNIAHMKAKGA"
## [2,] "4_70156404" "84" "43" "YHGIPMVGIPLFWDQPDNIAHMKAKGA"
## [3,] "4_70156404" "84" "43" "YHGIPMVGIPLFWDQPDNIAHMKAKGA"
## [4,] "4_70156404" "84" "43" "YHGIPMVGIPLFWDQPDNIAHMKAKGA"
## [5,] "4_70156404" "84" "43" "YHGIPMVGIPLFWDQPDNIAHMKAKGA"
## [6,] "4_70156404" "84" "43" "YHGIPMVGIPLFWDQPDNIAHMKAKGA"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA
## [1,] "YHGIPMVGIPFVLGSTX" "0" "NA" "NA"
## [2,] "YHGIPMVGIPFVLGSTX" "0" "NA" "NA"
## [3,] "YHGIPMVGIPFVLGSTX" "0" "NA" "NA"
## [4,] "YHGIPMVGIPFVLGSTX" "0" "NA" "NA"
## [5,] "YHGIPMVGIPFVLGSTX" "0" "NA" "NA"
## [6,] "YHGIPMVGIPFVLGSTX" "0" "NA" "NA"
## Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max P_I P_R P
## [1,] "0" "NA" "NA" "NA" "0" "0" "0"
## [2,] "0" "NA" "NA" "NA" "0" "0" "0"
## [3,] "0" "NA" "NA" "NA" "0" "0" "0"
## [4,] "0" "NA" "NA" "NA" "0" "0" "0"
## [5,] "0" "NA" "NA" "NA" "0" "0" "0"
## [6,] "0" "NA" "NA" "NA" "0" "0" "0"
print(Export_Summary_IndelSV(Input = Result_HLA1_INDEL_1, Mut_Rank_th = 5))
## Num_All_Alteration Num_Evaluated_Alteration
## 3 3
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 3 184
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 184 53
print(Export_Summary_IndelSV_perFragments(Input = Result_HLA1_INDEL_1, Mut_Rank_th = 5))
## YHGIPMVGIPFVLGSTX-0_UGT2B28
## Num_Peptide_Per_Pep 24.000
## Num_Cond_Peptide_Per_Pep 24.000
## Num_Rest_Peptide_Per_Pep 10.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.417
## -logP 0.391
## RDELLAAIKKFHIKVATQX-1_COL12A1
## Num_Peptide_Per_Pep 32.000
## Num_Cond_Peptide_Per_Pep 32.000
## Num_Rest_Peptide_Per_Pep 7.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.219
## -logP 0.437
## ARDFLPSLKNRFWKPSILPIFMYKHCSVQFSVRHGDVQTKVHX-2_SLCO1C1
## Num_Peptide_Per_Pep 128.000
## Num_Cond_Peptide_Per_Pep 128.000
## Num_Rest_Peptide_Per_Pep 36.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.281
## -logP 0.989
To calculate the binding affinity of neoantigen candaites, which are generated from from indels, to HLA ClassII.
Result_HLA2_INDEL <- MainINDELClass2(input_annovar_format_file = "./../data/sample_vcf.annovar.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c2.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCIIpan_dir = "./../lib/netMHCIIpan-4.3/netMHCIIpan",
depth_tumor_column = 12,
depth_normal_column = 14,
SNPs = "./../data/sample_vcf.snps.txt",
multiple_variants = TRUE)
## [1] "HLAtype: DPA1*01:03" "HLAtype: DPA1*02:01" "HLAtype: DPB1*02:01"
## [4] "HLAtype: DPB1*09:01" "HLAtype: DQA1*01:02" "HLAtype: DQA1*05:05"
## [7] "HLAtype: DQB1*03:01" "HLAtype: DQB1*06:04" "HLAtype: DRB1*11:04"
## [10] "HLAtype: DRB1*13:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Set depth_normal_column as 14 depth_normal"
## [1] "Set depth_tumor_column as 12 depth_tumor"
## [1] "Set nm_id_column as 10 AAChange.refGene"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tGeneDetail.refGene\tExonicFunc.refGene\tAAChange.refGene\tcytoBand\tdepth_tumor\tvariantNum_tumor\tdepth_normal"
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
## [1] "Start Analysis: Mutation 1"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 2"
## [1] "Peptide Successfully Generated!!"
## [1] "Start Analysis: Mutation 3"
## [1] "Peptide Successfully Generated!!"
## [1] "Peptide Successfully Generated!!"
## [1] "Peptide Successfully Generated!!"
## [1] "Peptide Successfully Generated!!"
## [1] "result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.txt.list.vcf"
## [1] "Executing netMHCpan to result.ID.INDEL2"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10201 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.1.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10901 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.2.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10201 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.3.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10901 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.4.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10301 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.5.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10604 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.6.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10301 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.7.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10604 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.8.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a DRB1_1104 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.9.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.peptide.fasta -a DRB1_1302 > result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.10.peptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.1.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.10.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.2.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.3.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.4.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.5.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.6.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.7.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.8.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.INDEL2/sample_vcf.annovar.txt.ID_INDEL.HLACLASS2.9.peptide.txt"
## [1] "33.3333333333333 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA2_INDEL <- CalculatePriorityScores(result = Result_HLA2_INDEL, useRNAvaf = FALSE)
print(head(Result_HLA2_INDEL))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core
## [1,] "DRB1_0101" "1" "0_UGT2B28" "YHGIPMVGI"
## [2,] "DRB1_0101" "2" "0_UGT2B28" "YHGIPMVGI"
## [3,] "DRB1_0101" "3" "0_UGT2B28" "YHGIPMVGI"
## [4,] "DRB1_0101" "4" "0_UGT2B28" "GIPMVGIPF"
## [5,] "DRB1_0101" "5" "0_UGT2B28" "MVGIPFVLG"
## [6,] "DRB1_0101" "6" "0_UGT2B28" "MVGIPFVLG"
## Evaluated_Mutant_Peptide Mut_EL Mut_Rank Chr NM_ID
## [1,] "YEAIYHGIPMVGIPF" "0.068310" "11.01" "4" "NM_053039"
## [2,] "EAIYHGIPMVGIPFV" "0.064542" "11.34" "4" "NM_053039"
## [3,] "AIYHGIPMVGIPFVL" "0.005254" "30.11" "4" "NM_053039"
## [4,] "IYHGIPMVGIPFVLG" "0.000447" "58.35" "4" "NM_053039"
## [5,] "YHGIPMVGIPFVLGS" "0.000776" "51.47" "4" "NM_053039"
## [6,] "HGIPMVGIPFVLGST" "0.001719" "41.82" "4" "NM_053039"
## Change Ref Alt Prob Mutation_Prob. Exon_Start Exon_End
## [1,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [2,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [3,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [4,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [5,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## [6,] "Out_c.1186dupT" "-" "T" "0" "0" "70146192" "70160768"
## Mutation_Position Total_Depth Tumor_Depth
## [1,] "4_70156404" "84" "43"
## [2,] "4_70156404" "84" "43"
## [3,] "4_70156404" "84" "43"
## [4,] "4_70156404" "84" "43"
## [5,] "4_70156404" "84" "43"
## [6,] "4_70156404" "84" "43"
## Wt_Peptide Mutant_Peptide Total_RNA
## [1,] "YEAIYHGIPMVGIPLFWDQPDNIAHMKAKGA" "YEAIYHGIPMVGIPFVLGSTX" "0"
## [2,] "YEAIYHGIPMVGIPLFWDQPDNIAHMKAKGA" "YEAIYHGIPMVGIPFVLGSTX" "0"
## [3,] "YEAIYHGIPMVGIPLFWDQPDNIAHMKAKGA" "YEAIYHGIPMVGIPFVLGSTX" "0"
## [4,] "YEAIYHGIPMVGIPLFWDQPDNIAHMKAKGA" "YEAIYHGIPMVGIPFVLGSTX" "0"
## [5,] "YEAIYHGIPMVGIPLFWDQPDNIAHMKAKGA" "YEAIYHGIPMVGIPFVLGSTX" "0"
## [6,] "YEAIYHGIPMVGIPLFWDQPDNIAHMKAKGA" "YEAIYHGIPMVGIPFVLGSTX" "0"
## Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio MutRatio_Min
## [1,] "NA" "NA" "0" "NA" "NA"
## [2,] "NA" "NA" "0" "NA" "NA"
## [3,] "NA" "NA" "0" "NA" "NA"
## [4,] "NA" "NA" "0" "NA" "NA"
## [5,] "NA" "NA" "0" "NA" "NA"
## [6,] "NA" "NA" "0" "NA" "NA"
## MutRatio_Max P_I P_R P
## [1,] "NA" "0" "0" "0"
## [2,] "NA" "0" "0" "0"
## [3,] "NA" "0" "0" "0"
## [4,] "NA" "0" "0" "0"
## [5,] "NA" "0" "0" "0"
## [6,] "NA" "0" "0" "0"
print(Export_Summary_IndelSV(Input = Result_HLA2_INDEL, , Mut_Rank_th = 10))
## Num_All_Alteration Num_Evaluated_Alteration
## 3 3
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 2 46
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 46 10
print(Export_Summary_IndelSV_perFragments(Input = Result_HLA2_INDEL, , Mut_Rank_th = 5))
## YEAIYHGIPMVGIPFVLGSTX-0_UGT2B28
## Num_Peptide_Per_Pep 6.000
## Num_Cond_Peptide_Per_Pep 6.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.483
## QYYQRDELLAAIKKFHIKVATQX-1_COL12A1
## Num_Peptide_Per_Pep 8.000
## Num_Cond_Peptide_Per_Pep 8.000
## Num_Rest_Peptide_Per_Pep 5.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.625
## -logP 0.529
## IMEMARDFLPSLKNRFWKPSILPIFMYKHCSVQFSVRHGDVQTKVHX-2_SLCO1C1
## Num_Peptide_Per_Pep 32.000
## Num_Cond_Peptide_Per_Pep 32.000
## Num_Rest_Peptide_Per_Pep 4.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.125
## -logP 1.081
To calculate the binding affinity of neoantigen candaites, which are generated from from SVs, to HLA ClassI.
Result_HLA1_SV <- MainSVFUSIONClass1(input_file = "./../data/sample_sv_bnd.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c1.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCpan_dir = "./../lib/netMHCpan-4.1/netMHCpan",
refdna_file = "./../lib/GRCh37.fa",
mutation_alt_bnd_column = 5,
gene_symbol_column = 7,
mate_id_column = 8)
## [1] "HLAtype: A*02:01" "HLAtype: A*32:01" "HLAtype: B*15:17" "HLAtype: B*51:01"
## [5] "HLAtype: C*07:01" "HLAtype: C*15:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Please Manually Indicate depth_normal_column if you want to use."
## [1] "Set depth_normal_column as NA NA"
## [1] "Please Manually Indicate depth_tumor_column if you want to use."
## [1] "Set depth_tumor_column as NA NA"
## [1] "Set nm_id_column as 0 "
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tmateID"
## [1] "Start Analysis: Mutation SVMERGE137"
## [1] "OK SVMERGE137"
## [1] "Start Analysis: Mutation SVMERGE15"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE15"
## [1] "Start Analysis: Mutation SVMERGE116"
## [1] "OK SVMERGE116"
## [1] "Start Analysis: Mutation SVMERGE3"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE3"
## [1] "Start Analysis: Mutation SVMERGE38"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE38"
## [1] "OK SVMERGE38"
## [1] "OK SVMERGE38"
## [1] "OK SVMERGE38"
## [1] "Start Analysis: Mutation SVMERGE195"
## [1] "OK SVMERGE195"
## [1] "OK SVMERGE195"
## [1] "Start Analysis: Mutation SVMERGE10"
## [1] "Start Analysis: Mutation SVMERGE272"
## [1] "OK SVMERGE272"
## [1] "Start Analysis: Mutation SVMERGE101"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE101"
## [1] "Start Analysis: Mutation SVMERGE40"
## [1] "OK SVMERGE40"
## [1] "Start Analysis: Mutation SVMERGE460"
## [1] "OK SVMERGE460"
## [1] "Start Analysis: Mutation SVMERGE133"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "OK SVMERGE133"
## [1] "Start Analysis: Mutation SVMERGE31"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE157"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE72"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE177"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE37"
## [1] "Non-Stop!!"
## [1] "Non-Stop!!"
## [1] "OK SVMERGE37"
## [1] "Start Analysis: Mutation SVMERGE206"
## [1] "OK SVMERGE206"
## [1] "Start Analysis: Mutation SVMERGE58"
## [1] "OK SVMERGE58"
## [1] "Start Analysis: Mutation SVMERGE210"
## [1] "OK SVMERGE210"
## [1] "Start Analysis: Mutation SVMERGE205"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.txt.list.vcf"
## [1] "Executing netMHCpan to result.ID.SV1"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a HLA-A02:01 > result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.1.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a HLA-A32:01 > result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.2.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a HLA-B15:17 > result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.3.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a HLA-B51:01 > result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.4.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a HLA-C07:01 > result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.5.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a HLA-C15:02 > result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.6.peptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.1.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.2.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.3.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.4.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.5.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV1/sample_sv_bnd.txt.ID_SVFusion.HLACLASS1.6.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA1_SV <- CalculatePriorityScores(result = Result_HLA1_SV, useRNAvaf = FALSE)
print(head(Result_HLA1_SV))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core
## [1,] "HLA-A*02:01" "1" "0_AAR2" "DYNSWEVGPKFRE"
## [2,] "HLA-A*02:01" "2" "0_AAR2" "YNSWEVGPKFREQ"
## [3,] "HLA-A*02:01" "3" "0_AAR2" "NSWEVGPKFREQL"
## [4,] "HLA-A*02:01" "4" "0_AAR2" "SWEVGPKFREQLK"
## [5,] "HLA-A*02:01" "5" "0_AAR2" "WEVGPKFREQLKL"
## [6,] "HLA-A*02:01" "6" "0_AAR2" "EVGPKFREQLKL"
## Evaluated_Mutant_Peptide Mut_EL Mut_Rank Chr NM_ID
## [1,] "DYNSWEVGPKFRE" "0.0000010" "95.000" "20" "NM_015511_NM_015906"
## [2,] "YNSWEVGPKFREQ" "0.0000080" "76.667" "20" "NM_015511_NM_015906"
## [3,] "NSWEVGPKFREQL" "0.0004280" "24.750" "20" "NM_015511_NM_015906"
## [4,] "SWEVGPKFREQLK" "0.0000030" "87.500" "20" "NM_015511_NM_015906"
## [5,] "WEVGPKFREQLKL" "0.0000430" "53.333" "20" "NM_015511_NM_015906"
## [6,] "EVGPKFREQLKLF" "0.0000060" "80.000" "20" "NM_015511_NM_015906"
## Change Ref Alt Prob Mutation_Prob.
## [1,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [2,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [3,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [4,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [5,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [6,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## Exon_Start Exon_End Mutation_Position Total_Depth Tumor_Depth
## [1,] "34824338" "34844863" "20_34827929" "0" "0"
## [2,] "34824338" "34844863" "20_34827929" "0" "0"
## [3,] "34824338" "34844863" "20_34827929" "0" "0"
## [4,] "34824338" "34844863" "20_34827929" "0" "0"
## [5,] "34824338" "34844863" "20_34827929" "0" "0"
## [6,] "34824338" "34844863" "20_34827929" "0" "0"
## Wt_Peptide
## [1,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [2,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [3,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [4,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [5,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [6,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA
## [1,] "DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE" "3.03498" "NA" "NA"
## [2,] "DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE" "3.03498" "NA" "NA"
## [3,] "DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE" "3.03498" "NA" "NA"
## [4,] "DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE" "3.03498" "NA" "NA"
## [5,] "DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE" "3.03498" "NA" "NA"
## [6,] "DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE" "3.03498" "NA" "NA"
## Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max
## [1,] "NaN" "NA" "NA" "NA"
## [2,] "NaN" "NA" "NA" "NA"
## [3,] "NaN" "NA" "NA" "NA"
## [4,] "NaN" "NA" "NA" "NA"
## [5,] "NaN" "NA" "NA" "NA"
## [6,] "NaN" "NA" "NA" "NA"
## P_I P_R P
## [1,] "0.994835363484567" "1.12475327099476e-202" "1.12475613722433e-202"
## [2,] "0.994835363426825" "7.25539311432306e-163" "7.25541160337557e-163"
## [3,] "0.994835359962294" "3.95361188289843e-50" "3.95362195796073e-50"
## [4,] "0.994835363468069" "2.17320320184772e-186" "2.17320873986164e-186"
## [5,] "0.994835363138115" "3.38686707516126e-112" "3.38687570597729e-112"
## [6,] "0.994835363443322" "4.19897614731469e-170" "4.19898684764329e-170"
print(Export_Summary_IndelSV(Result_HLA1_SV, , Mut_Rank_th = 5))
## Num_All_Alteration Num_Evaluated_Alteration
## 16 16
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 16 3183
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 3183 351
print(Export_Summary_IndelSV_perFragments(Result_HLA1_SV, , Mut_Rank_th = 5))
## DYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLE-0_AAR2
## Num_Peptide_Per_Pep 57.000
## Num_Cond_Peptide_Per_Pep 57.000
## Num_Rest_Peptide_Per_Pep 5.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.088
## -logP 0.782
## GDPHELRNIFLQLSAVQEAQLKRLEVTRPRVLGSREQGQVPRMARQPPPPWVHAAFLLCLLSLGG-1_SLC25A12
## Num_Peptide_Per_Pep 237.000
## Num_Cond_Peptide_Per_Pep 237.000
## Num_Rest_Peptide_Per_Pep 31.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.131
## -logP 1.496
## TMAEKRQLFIEMLYRLX-2_DTNB
## Num_Peptide_Per_Pep 24.000
## Num_Cond_Peptide_Per_Pep 24.000
## Num_Rest_Peptide_Per_Pep 7.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.292
## -logP 0.391
## TDWLSDCCFHPSERCRCTLYGHTDSVNSIEFFP-3_SPAG16
## Num_Peptide_Per_Pep 51.000
## Num_Cond_Peptide_Per_Pep 51.000
## Num_Rest_Peptide_Per_Pep 2.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.039
## -logP 0.759
## MKSCKRNLSTTTGSSERX-4_TMCC1
## Num_Peptide_Per_Pep 45.000
## Num_Cond_Peptide_Per_Pep 45.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.414
## ACLPGEEGTAERSCKRNLSTTTGSSERX-5_TMCC1
## Num_Peptide_Per_Pep 90.000
## Num_Cond_Peptide_Per_Pep 90.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.644
## VQRFSLRRQLSKSCKRNLSTTTGSSERX-6_TMCC1
## Num_Peptide_Per_Pep 90.000
## Num_Cond_Peptide_Per_Pep 90.000
## Num_Rest_Peptide_Per_Pep 3.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.033
## -logP 0.644
## QRKGSYCWDFEESCKRNLSTTTGSSERX-7_TMCC1
## Num_Peptide_Per_Pep 90.000
## Num_Cond_Peptide_Per_Pep 90.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.644
## IRPKPFVIPGRSRTLECKQQKIILLRREMKETX-8_PDLIM3
## Num_Peptide_Per_Pep 120.000
## Num_Cond_Peptide_Per_Pep 120.000
## Num_Rest_Peptide_Per_Pep 12.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.100
## -logP 0.759
## GQLRGLIPSSPQKTLECKQQKIILLRREMKETX-9_PDLIM3
## Num_Peptide_Per_Pep 120.000
## Num_Cond_Peptide_Per_Pep 120.000
## Num_Rest_Peptide_Per_Pep 19.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.158
## -logP 0.759
## GDQYIVDMANTKRTLLWTRPMTVILGKPFCVMPKQQKTAHIGFLQHIPRLSPKPCLPKLNLMMRKQRMSQNGKNVKFEESHLRAVCMSGRGMGQVWVFFLCSX-10_WDR70
## Num_Peptide_Per_Pep 540.00
## Num_Cond_Peptide_Per_Pep 540.00
## Num_Rest_Peptide_Per_Pep 81.00
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.15
## -logP 2.37
## LCPASRALEEKKGHELLGGPSLGAPRPGSQERTGENTAACQDHRFWAGQTAGCGRERIPCRRRQSAYQVDGIGINFTQNLYPPEX-11_EGFR
## Num_Peptide_Per_Pep 432.000
## Num_Cond_Peptide_Per_Pep 432.000
## Num_Rest_Peptide_Per_Pep 24.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.056
## -logP 1.956
## LTPMPEGLSQQQDMLKNTSKGHPDRLPLQMALT-12_ARHGEF10
## Num_Peptide_Per_Pep 51.000
## Num_Cond_Peptide_Per_Pep 51.000
## Num_Rest_Peptide_Per_Pep 3.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.059
## -logP 0.759
## PGVQGKKVRKPSPTTSASSSSWTSAGTSWPAGRRTGTATSGTATTTSVWPGCGTRMWSTQWSSVPRSRSCCSRPATTPPSKPGAPHAPCASSRHLAHGLAPSSPGLPARGAEVCWVHWSHRDPLRTSPGSVAFSRAGEVEMLIAVTPX-13_NOTCH1
## Num_Peptide_Per_Pep 810.000
## Num_Cond_Peptide_Per_Pep 810.000
## Num_Rest_Peptide_Per_Pep 97.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.120
## -logP 3.405
## SRGRGNNNRKGREVTPL-14_UBAP2
## Num_Peptide_Per_Pep 30.000
## Num_Cond_Peptide_Per_Pep 30.000
## Num_Rest_Peptide_Per_Pep 1.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.033
## -logP 0.391
## IPSSQLAAKLLHMLTMRMLSKSATGRWX-15_RASGRP2
## Num_Peptide_Per_Pep 90.000
## Num_Cond_Peptide_Per_Pep 90.000
## Num_Rest_Peptide_Per_Pep 20.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.222
## -logP 0.644
## RKSPPEKKLRRYPPGQGATIGVDFMIKTVEINGE-16_GAB2
## Num_Peptide_Per_Pep 57.000
## Num_Cond_Peptide_Per_Pep 57.000
## Num_Rest_Peptide_Per_Pep 11.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.193
## -logP 0.782
## MSVIVLPQPDEVLNLVQSYVTLRVPLYVSYVFH-17_MTRF1
## Num_Peptide_Per_Pep 51.000
## Num_Cond_Peptide_Per_Pep 51.000
## Num_Rest_Peptide_Per_Pep 12.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.235
## -logP 0.759
## LWKCLRKPVLNDRNLQLHTDKGSFLKEKNKKLKKK-18_EVI2B
## Num_Peptide_Per_Pep 63.000
## Num_Cond_Peptide_Per_Pep 63.000
## Num_Rest_Peptide_Per_Pep 8.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.127
## -logP 0.805
## RTFLQSTDPGDTGGVFEGSTLCPSDPAFSRTDDPX-19_IKZF3
## Num_Peptide_Per_Pep 132.000
## Num_Cond_Peptide_Per_Pep 132.000
## Num_Rest_Peptide_Per_Pep 9.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.068
## -logP 0.805
## RDALTGHLRTHSGGVFEGSTLCPSDPAFSRTDDPX-20_IKZF3
## Num_Peptide_Per_Pep 132.000
## Num_Cond_Peptide_Per_Pep 132.000
## Num_Rest_Peptide_Per_Pep 10.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.076
## -logP 0.805
## GEGPANEDEDIGGGVFEGSTLCPSDPAFSRTDDPX-21_IKZF3
## Num_Peptide_Per_Pep 132.000
## Num_Cond_Peptide_Per_Pep 132.000
## Num_Rest_Peptide_Per_Pep 5.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.038
## -logP 0.805
## NVLMVHKRSHTGGVFEGSTLCPSDPAFSRTDDPX-22_IKZF3
## Num_Peptide_Per_Pep 126.000
## Num_Cond_Peptide_Per_Pep 126.000
## Num_Rest_Peptide_Per_Pep 10.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.079
## -logP 0.782
## FNVLMVHKRSHTGGVFEGSTLCPSDPAFSRTDDPX-23_IKZF3
## Num_Peptide_Per_Pep 132.000
## Num_Cond_Peptide_Per_Pep 132.000
## Num_Rest_Peptide_Per_Pep 10.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.076
## -logP 0.805
To calculate the binding affinity of neoantigen candaites, which are generated from from SVs, to HLA ClassII.
Result_HLA2_SV <- MainSVFUSIONClass2(input_file = "./../data/sample_sv_bnd.txt",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c2.txt",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
rnaexp_file = "./../data/sample_rna_exp.txt",
netMHCIIpan_dir = "./../lib/netMHCIIpan-4.3/netMHCIIpan",
refdna_file = "./../lib/GRCh37.fa",
mutation_alt_bnd_column = 5,
gene_symbol_column = 7,
mate_id_column = 8)
## [1] "HLAtype: DPA1*01:03" "HLAtype: DPA1*02:01" "HLAtype: DPB1*02:01"
## [4] "HLAtype: DPB1*09:01" "HLAtype: DQA1*01:02" "HLAtype: DQA1*05:05"
## [7] "HLAtype: DQB1*03:01" "HLAtype: DQB1*06:04" "HLAtype: DRB1*11:04"
## [10] "HLAtype: DRB1*13:02"
## [1] "Set chr_column as 1 Chr"
## [1] "Set mutation_start_column as 2 Start"
## [1] "Set mutation_end_column as 3 End"
## [1] "Set mutation_ref_column as 4 Ref"
## [1] "Set mutation_alt_column as 5 Alt"
## [1] "Please Manually Indicate depth_normal_column if you want to use."
## [1] "Set depth_normal_column as NA NA"
## [1] "Please Manually Indicate depth_tumor_column if you want to use."
## [1] "Set depth_tumor_column as NA NA"
## [1] "Set nm_id_column as 0 "
## [1] "Please Confirm that Reading Start Line is 1"
## [1] "Chr\tStart\tEnd\tRef\tAlt\tFunc.refGene\tGene.refGene\tmateID"
## [1] "Start Analysis: Mutation SVMERGE137"
## [1] "OK SVMERGE137"
## [1] "Start Analysis: Mutation SVMERGE15"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE15"
## [1] "Start Analysis: Mutation SVMERGE116"
## [1] "OK SVMERGE116"
## [1] "Start Analysis: Mutation SVMERGE3"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE3"
## [1] "Start Analysis: Mutation SVMERGE38"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE38"
## [1] "OK SVMERGE38"
## [1] "OK SVMERGE38"
## [1] "OK SVMERGE38"
## [1] "Start Analysis: Mutation SVMERGE195"
## [1] "OK SVMERGE195"
## [1] "OK SVMERGE195"
## [1] "Start Analysis: Mutation SVMERGE10"
## [1] "Start Analysis: Mutation SVMERGE272"
## [1] "OK SVMERGE272"
## [1] "Start Analysis: Mutation SVMERGE101"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE101"
## [1] "Start Analysis: Mutation SVMERGE40"
## [1] "OK SVMERGE40"
## [1] "Start Analysis: Mutation SVMERGE460"
## [1] "OK SVMERGE460"
## [1] "Start Analysis: Mutation SVMERGE133"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "OK SVMERGE133"
## [1] "Start Analysis: Mutation SVMERGE31"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE157"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE72"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE177"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Annotation is Exonic but Position is Intronic"
## [1] "Start Analysis: Mutation SVMERGE37"
## [1] "Non-Stop!!"
## [1] "Non-Stop!!"
## [1] "OK SVMERGE37"
## [1] "Start Analysis: Mutation SVMERGE206"
## [1] "OK SVMERGE206"
## [1] "Start Analysis: Mutation SVMERGE58"
## [1] "OK SVMERGE58"
## [1] "Start Analysis: Mutation SVMERGE210"
## [1] "OK SVMERGE210"
## [1] "Start Analysis: Mutation SVMERGE205"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "Annotation is Intronic but Position is not Intron"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "OK SVMERGE205"
## [1] "result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.txt.list.vcf"
## [1] "Executing netMHCpan to result.ID.SV2"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10201 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.1.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10901 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.2.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10201 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.3.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10901 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.4.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10301 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.5.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10604 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.6.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10301 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.7.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10604 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.8.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a DRB1_1104 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.9.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.peptide.fasta -a DRB1_1302 > result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.10.peptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.1.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.10.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.2.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.3.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.4.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.5.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.6.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.7.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.8.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.ID.SV2/sample_sv_bnd.txt.ID_SVFusion.HLACLASS2.9.peptide.txt"
## [1] "4.16666666666667 perc. fin"
## [1] "8.33333333333333 perc. fin"
## [1] "12.5 perc. fin"
## [1] "16.6666666666667 perc. fin"
## [1] "20.8333333333333 perc. fin"
## [1] "25 perc. fin"
## [1] "29.1666666666667 perc. fin"
## [1] "33.3333333333333 perc. fin"
## [1] "37.5 perc. fin"
## [1] "41.6666666666667 perc. fin"
## [1] "45.8333333333333 perc. fin"
## [1] "50 perc. fin"
## [1] "54.1666666666667 perc. fin"
## [1] "58.3333333333333 perc. fin"
## [1] "62.5 perc. fin"
## [1] "66.6666666666667 perc. fin"
## [1] "70.8333333333333 perc. fin"
## [1] "75 perc. fin"
## [1] "79.1666666666667 perc. fin"
## [1] "83.3333333333333 perc. fin"
## [1] "87.5 perc. fin"
## [1] "91.6666666666667 perc. fin"
## [1] "95.8333333333333 perc. fin"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA2_SV <- CalculatePriorityScores(result = Result_HLA2_SV, useRNAvaf = FALSE)
print(head(Result_HLA2_SV))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core
## [1,] "DRB1_0101" "1" "0_AAR2" "YNSWEVGPK"
## [2,] "DRB1_0101" "2" "0_AAR2" "YNSWEVGPK"
## [3,] "DRB1_0101" "3" "0_AAR2" "YNSWEVGPK"
## [4,] "DRB1_0101" "4" "0_AAR2" "WEVGPKFRE"
## [5,] "DRB1_0101" "5" "0_AAR2" "WEVGPKFRE"
## [6,] "DRB1_0101" "6" "0_AAR2" "VGPKFREQL"
## Evaluated_Mutant_Peptide Mut_EL Mut_Rank Chr NM_ID
## [1,] "GIDYNSWEVGPKFRE" "0.002971" "35.75" "20" "NM_015511_NM_015906"
## [2,] "IDYNSWEVGPKFREQ" "0.000624" "54.09" "20" "NM_015511_NM_015906"
## [3,] "DYNSWEVGPKFREQL" "0.000203" "68.45" "20" "NM_015511_NM_015906"
## [4,] "YNSWEVGPKFREQLK" "0.000105" "76.22" "20" "NM_015511_NM_015906"
## [5,] "NSWEVGPKFREQLKL" "0.000042" "85.71" "20" "NM_015511_NM_015906"
## [6,] "SWEVGPKFREQLKLF" "0.000009" "95.50" "20" "NM_015511_NM_015906"
## Change Ref Alt Prob Mutation_Prob.
## [1,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [2,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [3,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [4,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [5,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## [6,] "In_AAR2_exon_TRIM33_exon" "G" "G]1:115005805]" "0" "0"
## Exon_Start Exon_End Mutation_Position Total_Depth Tumor_Depth
## [1,] "34824338" "34844863" "20_34827929" "0" "0"
## [2,] "34824338" "34844863" "20_34827929" "0" "0"
## [3,] "34824338" "34844863" "20_34827929" "0" "0"
## [4,] "34824338" "34844863" "20_34827929" "0" "0"
## [5,] "34824338" "34844863" "20_34827929" "0" "0"
## [6,] "34824338" "34844863" "20_34827929" "0" "0"
## Wt_Peptide
## [1,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [2,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [3,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [4,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [5,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## [6,] "MAAVQMDPELAKRLFFEGATVVILNMPKGTEFGIDYNSWEVGPKFRGVKMIPPGIHFLHYSSVDKANPKEVGPRMGFFLSLHQRGLTVLRWSTLREEVDLSPAPESEVEAMRANLQELDQFLGPYPYATLKKWISLTNFISEATVEKLQPENRQICAFSDVLPVLSMKHTKDRVGQNLPRCGIECKSYQEGLARLPEMKPRAGTEIRFSELPTQMFPEGATPAEITKHSMDLSYALETVLNKQFPSSPQDVLGELQFAFVCFLLGNVYEAFEHWKRLLNLLCRSEAAMMKHHTLYINLISILYHQLGEIPADFFVDIVSQDNFLTSTLQVFFSSACSIAVDATLRKKAEKFQAHLTKKFRWDFAAEPEDCAPVVVELPEGIEMGXXMAENKGGGEAESGGGGSGSAPVTAGAAGPAAQEAEPPLTAVLVEEEEEEGGRAGAEGGAAGPDDGGVAAASSGSAQAASSPAASVGTGVAGGAVSTPAPAPASAPAPGPSAGPPPGPPASLLDTCAVCQQSLQSRREAEPKLLPCLHSFCLRCLPEPERQLSVPIPGGSNGDIQQVGVIRCPVCRQECRQIDLVDNYFVKDTSEAPSSSDEKSEQVCTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHLIRKKEDVSESVGASGQRPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQKGAIENLLAKLLEKKNYVHFAATQVQNRIKEVNETNKRVEQEIKVAIFTLINEINKKGKSLLQQLENVTKERQMKLLQQQNDITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVVNLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINLAQLRLQHMQQQVYAQKHQQLQQMRMQQPPAPVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQYSMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSLPDIPPIQLEDAGSSSLDNLLSRYISGSHLPPQPTSTMNPSPGPSALSPGSSGLSNSHTPVRPPSTSSTGSRGSCGSSGRTAEKTSLSFKSDQVKVKQEPGTEDEICSFSGGVKQEKTEDGRRSACMLSSPESSLTPPLSTNLHLESELDALASLENHVKIEPADMNESCKQSGLSSLVNGKSPIRSLMHRSARIGGDGNNKDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLPEFEQEEDDGEVTEDSDEDFIQPRRKRLKSDERPVHIKX"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio
## [1,] "GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK" "3.03498" "NA"
## [2,] "GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK" "3.03498" "NA"
## [3,] "GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK" "3.03498" "NA"
## [4,] "GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK" "3.03498" "NA"
## [5,] "GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK" "3.03498" "NA"
## [6,] "GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK" "3.03498" "NA"
## Tumor_RNA Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max
## [1,] "NA" "NaN" "NA" "NA" "NA"
## [2,] "NA" "NaN" "NA" "NA" "NA"
## [3,] "NA" "NaN" "NA" "NA" "NA"
## [4,] "NA" "NaN" "NA" "NA" "NA"
## [5,] "NA" "NaN" "NA" "NA" "NA"
## [6,] "NA" "NaN" "NA" "NA" "NA"
## P_I P_R P
## [1,] "0.994835338984919" "5.13804056470373e-74" "5.13805365806756e-74"
## [2,] "0.994835358345505" "7.69118996528602e-114" "7.69120956488771e-114"
## [3,] "0.994835361818295" "5.05416874225877e-145" "5.05418162189048e-145"
## [4,] "0.994835362626685" "6.78124000735739e-162" "6.78125728811676e-162"
## [5,] "0.994835363146364" "1.67508152720577e-182" "1.67508579584702e-182"
## [6,] "0.994835363418576" "9.23253707018305e-204" "9.23256059762808e-204"
print(Export_Summary_IndelSV(Result_HLA2_SV, Mut_Rank_th = 5))
## Num_All_Alteration Num_Evaluated_Alteration
## 16 16
## Num_Alteration_Generating_NeoAg Num_All_Peptide
## 8 588
## Num_Evaluated_Peptide Num_Peptide_Generating_NeoAg
## 588 30
print(Export_Summary_IndelSV_perFragments(Result_HLA2_SV, Mut_Rank_th = 5))
## GIDYNSWEVGPKFREQLKLFCETCDRLTCRDCQLLEHK-0_AAR2
## Num_Peptide_Per_Pep 14.000
## Num_Cond_Peptide_Per_Pep 14.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.874
## KRGDPHELRNIFLQLSAVQEAQLKRLEVTRPRVLGSREQGQVPRMARQPPPPWVHAAFLLCLLSLGGAI-1_SLC25A12
## Num_Peptide_Per_Pep 44.000
## Num_Cond_Peptide_Per_Pep 44.000
## Num_Rest_Peptide_Per_Pep 3.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.068
## -logP 1.588
## RKTMAEKRQLFIEMLYRLX-2_DTNB
## Num_Peptide_Per_Pep 4.000
## Num_Cond_Peptide_Per_Pep 4.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.437
## GHTDWLSDCCFHPSERCRCTLYGHTDSVNSIEFFPFS-3_SPAG16
## Num_Peptide_Per_Pep 13.000
## Num_Cond_Peptide_Per_Pep 13.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.851
## MKSCKRNLSTTTGSSERX-4_TMCC1
## Num_Peptide_Per_Pep 3.000
## Num_Cond_Peptide_Per_Pep 3.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.414
## AAACLPGEEGTAERSCKRNLSTTTGSSERX-5_TMCC1
## Num_Peptide_Per_Pep 15.00
## Num_Cond_Peptide_Per_Pep 15.00
## Num_Rest_Peptide_Per_Pep 0.00
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.00
## -logP 0.69
## MVQRFSLRRQLSKSCKRNLSTTTGSSERX-6_TMCC1
## Num_Peptide_Per_Pep 14.000
## Num_Cond_Peptide_Per_Pep 14.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.667
## PMQRKGSYCWDFEESCKRNLSTTTGSSERX-7_TMCC1
## Num_Peptide_Per_Pep 15.00
## Num_Cond_Peptide_Per_Pep 15.00
## Num_Rest_Peptide_Per_Pep 0.00
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.00
## -logP 0.69
## HNIRPKPFVIPGRSRTLECKQQKIILLRREMKETX-8_PDLIM3
## Num_Peptide_Per_Pep 20.000
## Num_Cond_Peptide_Per_Pep 20.000
## Num_Rest_Peptide_Per_Pep 2.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.100
## -logP 0.805
## LHGQLRGLIPSSPQKTLECKQQKIILLRREMKETX-9_PDLIM3
## Num_Peptide_Per_Pep 20.000
## Num_Cond_Peptide_Per_Pep 20.000
## Num_Rest_Peptide_Per_Pep 2.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.100
## -logP 0.805
## IKGDQYIVDMANTKRTLLWTRPMTVILGKPFCVMPKQQKTAHIGFLQHIPRLSPKPCLPKLNLMMRKQRMSQNGKNVKFEESHLRAVCMSGRGMGQVWVFFLCSX-10_WDR70
## Num_Peptide_Per_Pep 90.000
## Num_Cond_Peptide_Per_Pep 90.000
## Num_Rest_Peptide_Per_Pep 16.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.178
## -logP 2.416
## AALCPASRALEEKKGHELLGGPSLGAPRPGSQERTGENTAACQDHRFWAGQTAGCGRERIPCRRRQSAYQVDGIGINFTQNLYPPEX-11_EGFR
## Num_Peptide_Per_Pep 72.000
## Num_Cond_Peptide_Per_Pep 72.000
## Num_Rest_Peptide_Per_Pep 1.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.014
## -logP 2.002
## AILTPMPEGLSQQQDMLKNTSKGHPDRLPLQMALTEL-12_ARHGEF10
## Num_Peptide_Per_Pep 13.000
## Num_Cond_Peptide_Per_Pep 13.000
## Num_Rest_Peptide_Per_Pep 1.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.077
## -logP 0.851
## LKPGVQGKKVRKPSPTTSASSSSWTSAGTSWPAGRRTGTATSGTATTTSVWPGCGTRMWSTQWSSVPRSRSCCSRPATTPPSKPGAPHAPCASSRHLAHGLAPSSPGLPARGAEVCWVHWSHRDPLRTSPGSVAFSRAGEVEMLIAVTPX-13_NOTCH1
## Num_Peptide_Per_Pep 135.000
## Num_Cond_Peptide_Per_Pep 135.000
## Num_Rest_Peptide_Per_Pep 1.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.007
## -logP 3.451
## ESSRGRGNNNRKGREVTPL-14_UBAP2
## Num_Peptide_Per_Pep 5.000
## Num_Cond_Peptide_Per_Pep 5.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.437
## WYIPSSQLAAKLLHMLTMRMLSKSATGRWX-15_RASGRP2
## Num_Peptide_Per_Pep 15.00
## Num_Cond_Peptide_Per_Pep 15.00
## Num_Rest_Peptide_Per_Pep 3.00
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.20
## -logP 0.69
## WLRKSPPEKKLRRYPPGQGATIGVDFMIKTVEINGEKV-16_GAB2
## Num_Peptide_Per_Pep 14.000
## Num_Cond_Peptide_Per_Pep 14.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.874
## GTMSVIVLPQPDEVLNLVQSYVTLRVPLYVSYVFHSP-17_MTRF1
## Num_Peptide_Per_Pep 13.000
## Num_Cond_Peptide_Per_Pep 13.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.851
## IVLWKCLRKPVLNDRNLQLHTDKGSFLKEKNKKLKKKNK-18_EVI2B
## Num_Peptide_Per_Pep 15.000
## Num_Cond_Peptide_Per_Pep 15.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.897
## RCRTFLQSTDPGDTGGVFEGSTLCPSDPAFSRTDDPX-19_IKZF3
## Num_Peptide_Per_Pep 22.000
## Num_Cond_Peptide_Per_Pep 22.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.851
## QRRDALTGHLRTHSGGVFEGSTLCPSDPAFSRTDDPX-20_IKZF3
## Num_Peptide_Per_Pep 22.000
## Num_Cond_Peptide_Per_Pep 22.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.851
## DSGEGPANEDEDIGGGVFEGSTLCPSDPAFSRTDDPX-21_IKZF3
## Num_Peptide_Per_Pep 22.000
## Num_Cond_Peptide_Per_Pep 22.000
## Num_Rest_Peptide_Per_Pep 0.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.000
## -logP 0.851
## SFNVLMVHKRSHTGGVFEGSTLCPSDPAFSRTDDPX-22_IKZF3
## Num_Peptide_Per_Pep 21.000
## Num_Cond_Peptide_Per_Pep 21.000
## Num_Rest_Peptide_Per_Pep 2.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.095
## -logP 0.828
## ISFNVLMVHKRSHTGGVFEGSTLCPSDPAFSRTDDPX-23_IKZF3
## Num_Peptide_Per_Pep 22.000
## Num_Cond_Peptide_Per_Pep 22.000
## Num_Rest_Peptide_Per_Pep 3.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.136
## -logP 0.851
To calculate the binding affinity of neoantigen candaites, which are directly generated from RNA sequences, to HLA ClassI. The peptides included in the original genes ("NM_003998", "NM_001165412") are removed from the results.
Result_HLA1_Seq <- MainSeqFragmentClass1(input_sequence = "atggcagaagatgatccatatttgggaaggcctgaaaaaatgtttcatttggatccttctttgactcatacaatatttaatc",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c1.txt",
hmdir = getwd(),
job_id = "NO_job_id",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
netMHCpan_dir = "./../lib/netMHCpan-4.1/netMHCpan",
reference_nm_id = c("NM_003998", "NM_001165412"))
## [1] "Sequence: atggcagaagatgatccatatttgggaaggcctgaaaaaatgtttcatttggatccttctttgactcatacaatatttaatc"
## [1] "HLAtype: A*02:01" "HLAtype: A*32:01" "HLAtype: B*15:17" "HLAtype: B*51:01"
## [5] "HLAtype: C*07:01" "HLAtype: C*15:02"
## [1] "refFLAT: ./../lib/refFlat.grch37.txt"
## [1] "refMrna: ./../lib/refMrna.grch37.fa"
## [1] "Wt-NM_ID: NM_003998" "Wt-NM_ID: NM_001165412"
## [1] "Wt-Gene Symbol: NA"
## [1] "Start Position of Reading Frame is: 1"
## [1] "Peptide Successfully Generated!!"
## [1] "Executing netMHCpan to result.NO_job_id.SeqFragment1"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.peptide.fasta -a HLA-A02:01 > result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.1.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.peptide.fasta -a HLA-A32:01 > result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.2.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.peptide.fasta -a HLA-B15:17 > result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.3.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.peptide.fasta -a HLA-B51:01 > result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.4.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.peptide.fasta -a HLA-C07:01 > result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.5.peptide.txt"
## [1] "./../lib/netMHCpan-4.1/netMHCpan -BA -l 8,9,10,11,12,13 -f result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.peptide.fasta -a HLA-C15:02 > result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.6.peptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.1.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.2.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.3.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.4.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.5.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment1/NO_job_id_SeqFragment.HLACLASS1.6.peptide.txt"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA1_Seq <- CalculatePriorityScores(result = Result_HLA1_Seq, useRNAvaf = FALSE)
## Warning in CalculatePriorityScores(result = Result_HLA1_Seq, useRNAvaf =
## FALSE): NAs introduced by coercion
print(head(Result_HLA1_Seq))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core
## [1,] "HLA-A*02:01" "1" "0_atggcagaag" "MAEDDPYLGRPEK"
## [2,] "HLA-A*02:01" "2" "0_atggcagaag" "AEDDPYLGRPEKM"
## [3,] "HLA-A*02:01" "3" "0_atggcagaag" "EDDPYLGRPEKMF"
## [4,] "HLA-A*02:01" "4" "0_atggcagaag" "DDPYLGRPEKMFH"
## [5,] "HLA-A*02:01" "5" "0_atggcagaag" "YLGRPEKMFHL"
## [6,] "HLA-A*02:01" "6" "0_atggcagaag" "YLGRPEKMFHL"
## Evaluated_Mutant_Peptide Mut_EL Mut_Rank Chr NM_ID ReadingFrame
## [1,] "MAEDDPYLGRPEK" "0.0000280" "59.545" "0" "" "1"
## [2,] "AEDDPYLGRPEKM" "0.0001790" "33.938" "0" "" "1"
## [3,] "EDDPYLGRPEKMF" "0.0000050" "82.500" "0" "" "1"
## [4,] "DDPYLGRPEKMFH" "0.0000010" "95.000" "0" "" "1"
## [5,] "DPYLGRPEKMFHL" "0.0001750" "34.214" "0" "" "1"
## [6,] "PYLGRPEKMFHLD" "0.0000040" "85.000" "0" "" "1"
## SequenceNumber Chrs NM_IDs GeneIDs
## [1,] "1" "chr4;chr4" "NM_003998;NM_001165412" "NFKB1;NFKB1"
## [2,] "1" "chr4;chr4" "NM_003998;NM_001165412" "NFKB1;NFKB1"
## [3,] "1" "chr4;chr4" "NM_003998;NM_001165412" "NFKB1;NFKB1"
## [4,] "1" "chr4;chr4" "NM_003998;NM_001165412" "NFKB1;NFKB1"
## [5,] "1" "chr4;chr4" "NM_003998;NM_001165412" "NFKB1;NFKB1"
## [6,] "1" "chr4;chr4" "NM_003998;NM_001165412" "NFKB1;NFKB1"
## Exon_Starts Exon_Ends GroupID NumOfPeptides
## [1,] "103422515;103422515" "103538459;103538459" "0_1" "27"
## [2,] "103422515;103422515" "103538459;103538459" "0_1" "27"
## [3,] "103422515;103422515" "103538459;103538459" "0_1" "27"
## [4,] "103422515;103422515" "103538459;103538459" "0_1" "27"
## [5,] "103422515;103422515" "103538459;103538459" "0_1" "27"
## [6,] "103422515;103422515" "103538459;103538459" "0_1" "27"
## NumOfStops
## [1,] "0"
## [2,] "0"
## [3,] "0"
## [4,] "0"
## [5,] "0"
## [6,] "0"
## Wt_Peptide
## [1,] "MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [2,] "MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [3,] "MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [4,] "MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [5,] "MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [6,] "MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA
## [1,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [2,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [3,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [4,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [5,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [6,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max P_I P_R P
## [1,] "NA" "NA" "NA" "NA" NA NA NA
## [2,] "NA" "NA" "NA" "NA" NA NA NA
## [3,] "NA" "NA" "NA" "NA" NA NA NA
## [4,] "NA" "NA" "NA" "NA" NA NA NA
## [5,] "NA" "NA" "NA" "NA" NA NA NA
## [6,] "NA" "NA" "NA" "NA" NA NA NA
print(Export_Summary_Fragments(Result_HLA1_Seq, Mut_Rank_th = 5))
## [[1]]
## atggcagaag
## Num_Peptide_Per_Grp 63.000
## Num_Cond_Peptide_Per_Grp 63.000
## Num_Rest_Peptide_Per_Grp 15.000
## Num_Rest_Peptide_Per_Grp / Num_Cond_Peptide_Per_Grp 0.238
## -logP 0.621
##
## [[2]]
##
## Num_Peptide_Per_NM 63.000
## Num_Cond_Peptide_Per_NM 63.000
## Num_Rest_Peptide_Per_NM 15.000
## Num_Rest_Peptide_Per_NM / Num_Cond_Peptide_Per_NM 0.238
## -logP 0.621
##
## [[3]]
## MAEDDPYLGRPEKMFHLDPSLTHTIFN-0_atggcagaag-0_1
## Num_Peptide_Per_Pep 63.000
## Num_Cond_Peptide_Per_Pep 63.000
## Num_Rest_Peptide_Per_Pep 15.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.238
## -logP 0.621
To calculate the binding affinity of neoantigen candaites, which are directly generated from RNA sequences, to HLA ClassII. The peptides included in the riginal genes ("NFKB1", "BCL3") are removed from the results.
Result_HLA2_Seq <- MainSeqFragmentClass2(input_sequence = "atggcagaagatgatccatatttgggaaggcctgaaaaaatgtttcatttggatccttctttgactcatacaatatttaatc",
file_name_in_hla_table = "sample",
hla_file = "./../data/sample_hla_table_c2.txt",
hmdir = getwd(),
job_id = "NO_job_id",
refflat_file = "./../lib/refFlat.grch37.txt",
refmrna_file = "./../lib/refMrna.grch37.fa",
netMHCIIpan_dir = "./../lib/netMHCIIpan-4.3/netMHCIIpan",
reference_gene_symbol = c("NFKB1", "BCL3"))
## [1] "Sequence: atggcagaagatgatccatatttgggaaggcctgaaaaaatgtttcatttggatccttctttgactcatacaatatttaatc"
## [1] "HLAtype: DPA1*01:03" "HLAtype: DPA1*02:01" "HLAtype: DPB1*02:01"
## [4] "HLAtype: DPB1*09:01" "HLAtype: DQA1*01:02" "HLAtype: DQA1*05:05"
## [7] "HLAtype: DQB1*03:01" "HLAtype: DQB1*06:04" "HLAtype: DRB1*11:04"
## [10] "HLAtype: DRB1*13:02"
## [1] "refFLAT: ./../lib/refFlat.grch37.txt"
## [1] "refMrna: ./../lib/refMrna.grch37.fa"
## [1] "Wt-NM_ID: NA"
## [1] "Wt-Gene Symbol: NFKB1" "Wt-Gene Symbol: BCL3"
## [1] "Start Position of Reading Frame is: 1"
## [1] "Peptide Successfully Generated!!"
## [1] "Executing netMHCpan to result.NO_job_id.SeqFragment2"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10201 > result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.1.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DPA10103 -choose -chb DPB10901 > result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.2.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10201 > result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.3.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DPA10201 -choose -chb DPB10901 > result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.4.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10301 > result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.5.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DQA10102 -choose -chb DQB10604 > result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.6.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10301 > result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.7.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -choose -cha DQA10505 -choose -chb DQB10604 > result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.8.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -a DRB1_1104 > result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.9.peptide.txt"
## [1] "./../lib/netMHCIIpan-4.3/netMHCIIpan -length 15 -f result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.peptide.fasta -a DRB1_1302 > result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.10.peptide.txt"
## [1] "Merging Results..."
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.1.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.10.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.2.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.3.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.4.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NA.NO_job_id_SeqFragment.HLACLASS2.9.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.5.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.6.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.7.peptide.txt"
## [1] "100 perc. fin"
## [1] "/Users/takanorihasegawa/Documents/GitHub/Neoantimon/vignettes/result.NO_job_id.SeqFragment2/NO_job_id_SeqFragment.HLACLASS2.8.peptide.txt"
## [1] "100 perc. fin"
## [1] "Successfully Finished."
Result_HLA2_Seq <- CalculatePriorityScores(result = Result_HLA2_Seq, useRNAvaf = FALSE)
## Warning in CalculatePriorityScores(result = Result_HLA2_Seq, useRNAvaf =
## FALSE): NAs introduced by coercion
print(head(Result_HLA2_Seq))
## HLA Pos Gene Evaluated_Mutant_Peptide_Core
## [1,] "DRB1_0101" "1" "0_atggcagaag" "PYLGRPEKM"
## [2,] "DRB1_0101" "2" "0_atggcagaag" "YLGRPEKMF"
## [3,] "DRB1_0101" "3" "0_atggcagaag" "YLGRPEKMF"
## [4,] "DRB1_0101" "4" "0_atggcagaag" "YLGRPEKMF"
## [5,] "DRB1_0101" "5" "0_atggcagaag" "YLGRPEKMF"
## [6,] "DRB1_0101" "6" "0_atggcagaag" "GRPEKMFHL"
## Evaluated_Mutant_Peptide Mut_EL Mut_Rank Chr NM_ID ReadingFrame
## [1,] "MAEDDPYLGRPEKMF" "0.000116" "74.92" "0" "" "1"
## [2,] "AEDDPYLGRPEKMFH" "0.000639" "53.83" "0" "" "1"
## [3,] "EDDPYLGRPEKMFHL" "0.000790" "51.22" "0" "" "1"
## [4,] "DDPYLGRPEKMFHLD" "0.001267" "45.36" "0" "" "1"
## [5,] "DPYLGRPEKMFHLDP" "0.000216" "67.70" "0" "" "1"
## [6,] "PYLGRPEKMFHLDPS" "0.000048" "84.48" "0" "" "1"
## SequenceNumber Chrs
## [1,] "1" "chr19;chr4;chr4;chr4;chr4;chr4;chr4;chr4"
## [2,] "1" "chr19;chr4;chr4;chr4;chr4;chr4;chr4;chr4"
## [3,] "1" "chr19;chr4;chr4;chr4;chr4;chr4;chr4;chr4"
## [4,] "1" "chr19;chr4;chr4;chr4;chr4;chr4;chr4;chr4"
## [5,] "1" "chr19;chr4;chr4;chr4;chr4;chr4;chr4;chr4"
## [6,] "1" "chr19;chr4;chr4;chr4;chr4;chr4;chr4;chr4"
## NM_IDs
## [1,] "NM_005178;NM_001319226;NM_003998;NM_001165412;NM_001382626;NM_001382627;NM_001382628;NM_001382625"
## [2,] "NM_005178;NM_001319226;NM_003998;NM_001165412;NM_001382626;NM_001382627;NM_001382628;NM_001382625"
## [3,] "NM_005178;NM_001319226;NM_003998;NM_001165412;NM_001382626;NM_001382627;NM_001382628;NM_001382625"
## [4,] "NM_005178;NM_001319226;NM_003998;NM_001165412;NM_001382626;NM_001382627;NM_001382628;NM_001382625"
## [5,] "NM_005178;NM_001319226;NM_003998;NM_001165412;NM_001382626;NM_001382627;NM_001382628;NM_001382625"
## [6,] "NM_005178;NM_001319226;NM_003998;NM_001165412;NM_001382626;NM_001382627;NM_001382628;NM_001382625"
## GeneIDs
## [1,] "BCL3;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1"
## [2,] "BCL3;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1"
## [3,] "BCL3;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1"
## [4,] "BCL3;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1"
## [5,] "BCL3;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1"
## [6,] "BCL3;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1;NFKB1"
## Exon_Starts
## [1,] "45251964;103423090;103422515;103422515;103422515;103422515;103422515;103423090"
## [2,] "45251964;103423090;103422515;103422515;103422515;103422515;103422515;103423090"
## [3,] "45251964;103423090;103422515;103422515;103422515;103422515;103422515;103423090"
## [4,] "45251964;103423090;103422515;103422515;103422515;103422515;103422515;103423090"
## [5,] "45251964;103423090;103422515;103422515;103422515;103422515;103422515;103423090"
## [6,] "45251964;103423090;103422515;103422515;103422515;103422515;103422515;103423090"
## Exon_Ends
## [1,] "45263301;103538459;103538459;103538459;103538459;103538459;103538459;103538459"
## [2,] "45263301;103538459;103538459;103538459;103538459;103538459;103538459;103538459"
## [3,] "45263301;103538459;103538459;103538459;103538459;103538459;103538459;103538459"
## [4,] "45263301;103538459;103538459;103538459;103538459;103538459;103538459;103538459"
## [5,] "45263301;103538459;103538459;103538459;103538459;103538459;103538459;103538459"
## [6,] "45263301;103538459;103538459;103538459;103538459;103538459;103538459;103538459"
## GroupID NumOfPeptides NumOfStops
## [1,] "0_1" "27" "0"
## [2,] "0_1" "27" "0"
## [3,] "0_1" "27" "0"
## [4,] "0_1" "27" "0"
## [5,] "0_1" "27" "0"
## [6,] "0_1" "27" "0"
## Wt_Peptide
## [1,] "MPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [2,] "MPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [3,] "MPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [4,] "MPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [5,] "MPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## [6,] "MPRCPAGAMDEGPVDLRTRPKAAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVVPLDPLRGGCDLPAVPGPPHGLARPEALYYPGALLPLYPTRAMGSPFPLVNLPTPLYPMMCPMEHPLSADIAMATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRSGADSSLKNCHNDTPLMVARSRRVIDILRGKATRPASTSQPDPSPDRSANTSPESSSRLSSNGLLSASPSSSPSQSPPRDPPGFPMAPPNFFLPSPSPPAFLPFAGVLRGPGRPVPPSPAPGGSXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIXXMAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKIX"
## Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA
## [1,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [2,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [3,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [4,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [5,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## [6,] "MAEDDPYLGRPEKMFHLDPSLTHTIFN" "NA" "NA" "NA"
## Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max P_I P_R P
## [1,] "NA" "NA" "NA" "NA" NA NA NA
## [2,] "NA" "NA" "NA" "NA" NA NA NA
## [3,] "NA" "NA" "NA" "NA" NA NA NA
## [4,] "NA" "NA" "NA" "NA" NA NA NA
## [5,] "NA" "NA" "NA" "NA" NA NA NA
## [6,] "NA" "NA" "NA" "NA" NA NA NA
print(Export_Summary_Fragments(Result_HLA2_Seq, Mut_Rank_th = 5))
## [[1]]
## atggcagaag
## Num_Peptide_Per_Grp 13.000
## Num_Cond_Peptide_Per_Grp 13.000
## Num_Rest_Peptide_Per_Grp 3.000
## Num_Rest_Peptide_Per_Grp / Num_Cond_Peptide_Per_Grp 0.231
## -logP 0.621
##
## [[2]]
##
## Num_Peptide_Per_NM 13.000
## Num_Cond_Peptide_Per_NM 13.000
## Num_Rest_Peptide_Per_NM 3.000
## Num_Rest_Peptide_Per_NM / Num_Cond_Peptide_Per_NM 0.231
## -logP 0.621
##
## [[3]]
## MAEDDPYLGRPEKMFHLDPSLTHTIFN-0_atggcagaag-0_1
## Num_Peptide_Per_Pep 13.000
## Num_Cond_Peptide_Per_Pep 13.000
## Num_Rest_Peptide_Per_Pep 3.000
## Num_Rest_Peptide_Per_Pep / Num_Cond_Peptide_Per_Pep 0.231
## -logP 0.621
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