protr: Generating Various Numerical Representation Schemes of Protein Sequence

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Comprehensive toolkit for generating various numerical representation schemes of protein sequence. The descriptors and similarity scores included are extensively used in bioinformatics and chemogenomics. For full functionality, the software 'ncbi-blast+' is needed, see <http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download> for more information.

Author
Nan Xiao <me@nanx.me>, Qingsong Xu <qsxu@csu.edu.cn>, Dongsheng Cao
Date of publication
2016-11-12 19:55:11
Maintainer
Nan Xiao <me@nanx.me>
License
BSD 3-clause License + file LICENSE
Version
1.2-0
URLs

View on CRAN

Man pages

AA2DACOR
2D Autocorrelations Descriptors for 20 Amino Acids calculated...
AA3DMoRSE
3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon
AAACF
Atom-Centred Fragments Descriptors for 20 Amino Acids...
AABLOSUM100
BLOSUM100 Matrix for 20 Amino Acids
AABLOSUM45
BLOSUM45 Matrix for 20 Amino Acids
AABLOSUM50
BLOSUM50 Matrix for 20 Amino Acids
AABLOSUM62
BLOSUM62 Matrix for 20 Amino Acids
AABLOSUM80
BLOSUM80 Matrix for 20 Amino Acids
AABurden
Burden Eigenvalues Descriptors for 20 Amino Acids calculated...
AAConn
Connectivity Indices Descriptors for 20 Amino Acids...
AAConst
Constitutional Descriptors for 20 Amino Acids calculated by...
AACPSA
CPSA Descriptors for 20 Amino Acids calculated by Discovery...
AADescAll
All 2D Descriptors for 20 Amino Acids calculated by Dragon
AAEdgeAdj
Edge Adjacency Indices Descriptors for 20 Amino Acids...
AAEigIdx
Eigenvalue-Based Indices Descriptors for 20 Amino Acids...
AAFGC
Functional Group Counts Descriptors for 20 Amino Acids...
AAGeom
Geometrical Descriptors for 20 Amino Acids calculated by...
AAGETAWAY
GETAWAY Descriptors for 20 Amino Acids calculated by Dragon
AAindex
AAindex Data of 544 Physicochemical and Biological Properties...
AAInfo
Information Indices Descriptors for 20 Amino Acids calculated...
AAMetaInfo
Meta Information for the 20 Amino Acids
AAMOE2D
2D Descriptors for 20 Amino Acids calculated by MOE 2011.10
AAMOE3D
3D Descriptors for 20 Amino Acids calculated by MOE 2011.10
AAMolProp
Molecular Properties Descriptors for 20 Amino Acids...
AAPAM120
PAM120 Matrix for 20 Amino Acids
AAPAM250
PAM250 Matrix for 20 Amino Acids
AAPAM30
PAM30 Matrix for 20 Amino Acids
AAPAM40
PAM40 Matrix for 20 Amino Acids
AAPAM70
PAM70 Matrix for 20 Amino Acids
AARandic
Randic Molecular Profiles Descriptors for 20 Amino Acids...
AARDF
RDF Descriptors for 20 Amino Acids calculated by Dragon
AATopo
Topological Descriptors for 20 Amino Acids calculated by...
AATopoChg
Topological Charge Indices Descriptors for 20 Amino Acids...
AAWalk
Walk and Path Counts Descriptors for 20 Amino Acids...
AAWHIM
WHIM Descriptors for 20 Amino Acids calculated by Dragon
acc
Auto Cross Covariance (ACC) for Generating Scales-Based...
extractAAC
Amino Acid Composition Descriptor
extractAPAAC
Amphiphilic Pseudo Amino Acid Composition Descriptor
extractBLOSUM
BLOSUM and PAM Matrix-Derived Descriptors
extractCTDC
CTD Descriptors - Composition
extractCTDCClass
CTD Descriptors - Composition (with Customized Amino Acid...
extractCTDD
CTD Descriptors - Distribution
extractCTDDClass
CTD Descriptors - Distribution (with Customized Amino Acid...
extractCTDT
CTD Descriptors - Transition
extractCTDTClass
CTD Descriptors - Transition (with Customized Amino Acid...
extractCTriad
Conjoint Triad Descriptor
extractCTriadClass
Conjoint Triad Descriptor (with Customized Amino Acid...
extractDC
Dipeptide Composition Descriptor
extractDescScales
Scales-Based Descriptors with 20+ classes of Molecular...
extractFAScales
Scales-Based Descriptors derived by Factor Analysis
extractGeary
Geary Autocorrelation Descriptor
extractMDSScales
Scales-Based Descriptors derived by Multidimensional Scaling
extractMoran
Moran Autocorrelation Descriptor
extractMoreauBroto
Normalized Moreau-Broto Autocorrelation Descriptor
extractPAAC
Pseudo Amino Acid Composition Descriptor
extractProtFP
Amino Acid Properties Based Scales Descriptors (Protein...
extractProtFPGap
Amino Acid Properties Based Scales Descriptors (Protein...
extractPSSM
Compute PSSM (Position-Specific Scoring Matrix) for given...
extractPSSMAcc
Profile-based protein representation derived by PSSM...
extractPSSMFeature
Profile-based protein representation derived by PSSM...
extractQSO
Quasi-Sequence-Order (QSO) Descriptor
extractScales
Scales-Based Descriptors derived by Principal Components...
extractScalesGap
Scales-Based Descriptors derived by Principal Components...
extractSOCN
Sequence-Order-Coupling Numbers
extractTC
Tripeptide Composition Descriptor
getUniProt
Get Protein Sequences from UniProt by Protein ID
OptAA3d
OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10...
parGOSim
Protein Sequence Similarity Calculation based on Gene...
parSeqSim
Parallellized Protein Sequence Similarity Calculation based...
protcheck
Check if the protein sequence's amino acid types are in the...
protr-package
Generating Various Numerical Representation Schemes of...
protseg
Protein Sequence Segmentation
readFASTA
Read Protein Sequences in FASTA Format
readPDB
Read Protein Sequences in PDB Format
twoGOSim
Protein Similarity Calculation based on Gene Ontology (GO)...
twoSeqSim
Protein Sequence Alignment for Two Protein Sequences

Files in this package

protr
protr/inst
protr/inst/CITATION
protr/inst/sysdata
protr/inst/sysdata/Schneider-Wrede.csv
protr/inst/sysdata/AAidx.csv
protr/inst/sysdata/OptAA3d.sdf
protr/inst/sysdata/Grantham.csv
protr/inst/doc
protr/inst/doc/protr.pdf
protr/inst/doc/protr.R
protr/inst/doc/protr.Rnw
protr/inst/protseq
protr/inst/protseq/extracell.fasta
protr/inst/protseq/P20160.fasta
protr/inst/protseq/P10323.fasta
protr/inst/protseq/mitochondrion.fasta
protr/inst/protseq/align.fasta
protr/inst/protseq/P08218.fasta
protr/inst/protseq/4HHB.pdb
protr/inst/protseq/P00750.fasta
protr/inst/protseq/Plasminogen.fasta
protr/inst/protseq/Q9NZP8.fasta
protr/NAMESPACE
protr/NEWS.md
protr/data
protr/data/AAPAM70.rda
protr/data/AAMOE3D.rda
protr/data/AAWHIM.rda
protr/data/AARandic.rda
protr/data/AAMolProp.rda
protr/data/AABurden.rda
protr/data/AAindex.rda
protr/data/AAPAM30.rda
protr/data/AAPAM250.rda
protr/data/AATopoChg.rda
protr/data/AAEigIdx.rda
protr/data/AAFGC.rda
protr/data/AA3DMoRSE.rda
protr/data/AABLOSUM45.rda
protr/data/AAInfo.rda
protr/data/AABLOSUM100.rda
protr/data/AARDF.rda
protr/data/AATopo.rda
protr/data/AADescAll.rda
protr/data/AAConn.rda
protr/data/AAMetaInfo.rda
protr/data/AAPAM120.rda
protr/data/AABLOSUM80.rda
protr/data/AAWalk.rda
protr/data/AAEdgeAdj.rda
protr/data/AAACF.rda
protr/data/AAMOE2D.rda
protr/data/AAGeom.rda
protr/data/AACPSA.rda
protr/data/AAConst.rda
protr/data/AABLOSUM50.rda
protr/data/AAGETAWAY.rda
protr/data/AA2DACOR.rda
protr/data/AAPAM40.rda
protr/data/AABLOSUM62.rda
protr/R
protr/R/misc04protseg.R
protr/R/desc15PSSMAcc.R
protr/R/desc05Moran.R
protr/R/desc10CTriad.R
protr/R/pcm02extractDescScales.R
protr/R/pcm01extractScales.R
protr/R/desc06Geary.R
protr/R/pcm05extractMDSScales.R
protr/R/pcm03extractProtFPGap.R
protr/R/desc15PSSMFeature.R
protr/R/desc08CTDT.R
protr/R/misc03protcheck.R
protr/R/misc06acc.R
protr/R/misc02readPDB.R
protr/R/desc01AAC.R
protr/R/pcm01extractScalesGap.R
protr/R/misc01readFASTA.R
protr/R/protr-package.R
protr/R/pcm06extractBLOSUM.R
protr/R/protr-datalist.R
protr/R/desc09CTDD.R
protr/R/desc09CTDDClass.R
protr/R/pcm03extractProtFP.R
protr/R/pcm04extractFAScales.R
protr/R/desc02DC.R
protr/R/desc15PSSM.R
protr/R/desc08CTDTClass.R
protr/R/desc07CTDC.R
protr/R/desc14APAAC.R
protr/R/desc04MoreauBroto.R
protr/R/par02parGOSim.R
protr/R/misc05getUniProt.R
protr/R/desc03TC.R
protr/R/desc07CTDCClass.R
protr/R/desc10CTriadClass.R
protr/R/desc11SOCN.R
protr/R/desc12QSO.R
protr/R/par01parSeqSim.R
protr/R/desc13PAAC.R
protr/vignettes
protr/vignettes/protr.bib
protr/vignettes/fig
protr/vignettes/fig/APAAC.pdf
protr/vignettes/fig/roc.pdf
protr/vignettes/fig/QSO.png
protr/vignettes/fig/protrweb.png
protr/vignettes/fig/PAAC.png
protr/vignettes/fig/AAindex.pdf
protr/vignettes/fig/logo-panel-text.pdf
protr/vignettes/fig/CTD.pdf
protr/vignettes/fig/ctriad.pdf
protr/vignettes/protr.Rnw
protr/README.md
protr/MD5
protr/build
protr/build/vignette.rds
protr/DESCRIPTION
protr/man
protr/man/extractBLOSUM.Rd
protr/man/AAPAM40.Rd
protr/man/extractGeary.Rd
protr/man/AABLOSUM62.Rd
protr/man/extractPSSMAcc.Rd
protr/man/parSeqSim.Rd
protr/man/AABurden.Rd
protr/man/parGOSim.Rd
protr/man/AADescAll.Rd
protr/man/extractPAAC.Rd
protr/man/extractMDSScales.Rd
protr/man/AABLOSUM80.Rd
protr/man/extractScalesGap.Rd
protr/man/extractPSSMFeature.Rd
protr/man/extractCTDDClass.Rd
protr/man/AAEdgeAdj.Rd
protr/man/AAConn.Rd
protr/man/extractProtFP.Rd
protr/man/OptAA3d.Rd
protr/man/AAindex.Rd
protr/man/readFASTA.Rd
protr/man/extractAPAAC.Rd
protr/man/AARDF.Rd
protr/man/readPDB.Rd
protr/man/extractCTDT.Rd
protr/man/protseg.Rd
protr/man/extractPSSM.Rd
protr/man/extractCTDCClass.Rd
protr/man/AABLOSUM45.Rd
protr/man/extractSOCN.Rd
protr/man/acc.Rd
protr/man/AAPAM30.Rd
protr/man/extractMoran.Rd
protr/man/protr-package.Rd
protr/man/extractCTDTClass.Rd
protr/man/extractMoreauBroto.Rd
protr/man/AAWHIM.Rd
protr/man/AAGeom.Rd
protr/man/extractCTDD.Rd
protr/man/AAPAM70.Rd
protr/man/AAEigIdx.Rd
protr/man/AAPAM250.Rd
protr/man/AAMOE2D.Rd
protr/man/AA3DMoRSE.Rd
protr/man/AABLOSUM50.Rd
protr/man/AAMolProp.Rd
protr/man/AACPSA.Rd
protr/man/AAInfo.Rd
protr/man/extractCTriadClass.Rd
protr/man/AAPAM120.Rd
protr/man/twoSeqSim.Rd
protr/man/extractTC.Rd
protr/man/extractQSO.Rd
protr/man/extractFAScales.Rd
protr/man/extractCTriad.Rd
protr/man/protcheck.Rd
protr/man/AARandic.Rd
protr/man/twoGOSim.Rd
protr/man/AAGETAWAY.Rd
protr/man/extractProtFPGap.Rd
protr/man/extractCTDC.Rd
protr/man/AA2DACOR.Rd
protr/man/extractDC.Rd
protr/man/AAACF.Rd
protr/man/extractDescScales.Rd
protr/man/AAWalk.Rd
protr/man/AAMOE3D.Rd
protr/man/AAConst.Rd
protr/man/AATopo.Rd
protr/man/AAFGC.Rd
protr/man/AABLOSUM100.Rd
protr/man/extractAAC.Rd
protr/man/AAMetaInfo.Rd
protr/man/getUniProt.Rd
protr/man/extractScales.Rd
protr/man/AATopoChg.Rd
protr/LICENSE