protr: Generating Various Numerical Representation Schemes for Protein Sequences

Comprehensive toolkit for generating various numerical features of protein sequences described in Xiao et al. (2015) <DOI:10.1093/bioinformatics/btv042>. For full functionality, the software 'ncbi-blast+' is needed, see <https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download> for more information.

Install the latest version of this package by entering the following in R:
install.packages("protr")
AuthorNan Xiao [aut, cre], Qingsong Xu [aut], Dongsheng Cao [aut]
Date of publication2016-12-30 10:12:29
MaintainerNan Xiao <me@nanx.me>
LicenseBSD_3_clause + file LICENSE
Version1.2-1
http://nanx.me/protr/
https://github.com/road2stat/protr, http://protr.org

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 for...

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

Functions

AA2DACOR Man page
AA3DMoRSE Man page
AAACF Man page
AABLOSUM100 Man page
AABLOSUM45 Man page
AABLOSUM50 Man page
AABLOSUM62 Man page
AABLOSUM80 Man page
AABurden Man page
AAConn Man page
AAConst Man page
AACPSA Man page
AADescAll Man page
AAEdgeAdj Man page
AAEigIdx Man page
AAFGC Man page
AAGeom Man page
AAGETAWAY Man page
AAindex Man page
AAInfo Man page
AAMetaInfo Man page
AAMOE2D Man page
AAMOE3D Man page
AAMolProp Man page
AAPAM120 Man page
AAPAM250 Man page
AAPAM30 Man page
AAPAM40 Man page
AAPAM70 Man page
AARandic Man page
AARDF Man page
AATopo Man page
AATopoChg Man page
AAWalk Man page
AAWHIM Man page
acc Man page
extractAAC Man page
extractAPAAC Man page
extractBLOSUM Man page
extractCTDC Man page
extractCTDCClass Man page
extractCTDD Man page
extractCTDDClass Man page
extractCTDT Man page
extractCTDTClass Man page
extractCTriad Man page
extractCTriadClass Man page
extractDC Man page
extractDescScales Man page
extractFAScales Man page
extractGeary Man page
extractMDSScales Man page
extractMoran Man page
extractMoreauBroto Man page
extractPAAC Man page
extractProtFP Man page
extractProtFPGap Man page
extractPSSM Man page
extractPSSMAcc Man page
extractPSSMFeature Man page
extractQSO Man page
extractScales Man page
extractScalesGap Man page
extractSOCN Man page
extractTC Man page
getUniProt Man page
OptAA3d Man page
parGOSim Man page
parSeqSim Man page
protcheck Man page
protr Man page
protr-package Man page
protseg Man page
readFASTA Man page
readPDB Man page
twoGOSim Man page
twoSeqSim Man page

Files

inst
inst/CITATION
inst/sysdata
inst/sysdata/Schneider-Wrede.csv
inst/sysdata/AAidx.csv
inst/sysdata/OptAA3d.sdf
inst/sysdata/Grantham.csv
inst/doc
inst/doc/protr.pdf
inst/doc/protr.R
inst/doc/protr.Rnw
inst/protseq
inst/protseq/extracell.fasta
inst/protseq/P20160.fasta
inst/protseq/P10323.fasta
inst/protseq/mitochondrion.fasta
inst/protseq/align.fasta
inst/protseq/P08218.fasta
inst/protseq/4HHB.pdb
inst/protseq/P00750.fasta
inst/protseq/Plasminogen.fasta
inst/protseq/Q9NZP8.fasta
NAMESPACE
NEWS.md
data
data/AAPAM70.rda
data/AAMOE3D.rda
data/AAWHIM.rda
data/AARandic.rda
data/AAMolProp.rda
data/AABurden.rda
data/AAindex.rda
data/AAPAM30.rda
data/AAPAM250.rda
data/AATopoChg.rda
data/AAEigIdx.rda
data/AAFGC.rda
data/AA3DMoRSE.rda
data/AABLOSUM45.rda
data/AAInfo.rda
data/AABLOSUM100.rda
data/AARDF.rda
data/AATopo.rda
data/AADescAll.rda
data/AAConn.rda
data/AAMetaInfo.rda
data/AAPAM120.rda
data/AABLOSUM80.rda
data/AAWalk.rda
data/AAEdgeAdj.rda
data/AAACF.rda
data/AAMOE2D.rda
data/AAGeom.rda
data/AACPSA.rda
data/AAConst.rda
data/AABLOSUM50.rda
data/AAGETAWAY.rda
data/AA2DACOR.rda
data/AAPAM40.rda
data/AABLOSUM62.rda
R
R/pcm-01-extractScalesGap.R R/desc-09-CTDD.R R/misc-06-acc.R R/desc-07-CTDCClass.R R/misc-03-protcheck.R R/pcm-04-extractFAScales.R R/desc-07-CTDC.R R/misc-01-readFASTA.R R/desc-14-APAAC.R R/desc-08-CTDTClass.R R/pcm-05-extractMDSScales.R R/desc-09-CTDDClass.R R/desc-01-AAC.R R/par-02-parGOSim.R R/desc-06-Geary.R R/misc-04-protseg.R R/protr-package.R R/pcm-01-extractScales.R R/desc-13-PAAC.R R/desc-15-PSSMFeature.R R/pcm-03-extractProtFPGap.R R/pcm-06-extractBLOSUM.R R/pcm-02-extractDescScales.R R/protr-datalist.R R/desc-03-TC.R R/desc-04-MoreauBroto.R R/desc-12-QSO.R R/desc-15-PSSM.R R/desc-10-CTriadClass.R R/desc-08-CTDT.R R/misc-02-readPDB.R R/desc-15-PSSMAcc.R R/par-01-parSeqSim.R R/desc-05-Moran.R R/desc-02-DC.R R/pcm-03-extractProtFP.R R/desc-10-CTriad.R R/misc-05-getUniProt.R R/desc-11-SOCN.R
vignettes
vignettes/protr.bib
vignettes/fig
vignettes/fig/APAAC.pdf
vignettes/fig/roc.pdf
vignettes/fig/QSO.png
vignettes/fig/protrweb.png
vignettes/fig/PAAC.png
vignettes/fig/AAindex.pdf
vignettes/fig/logo-panel-text.pdf
vignettes/fig/CTD.pdf
vignettes/fig/ctriad.pdf
vignettes/protr.Rnw
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/extractBLOSUM.Rd man/AAPAM40.Rd man/extractGeary.Rd man/AABLOSUM62.Rd man/extractPSSMAcc.Rd man/parSeqSim.Rd man/AABurden.Rd man/parGOSim.Rd man/AADescAll.Rd man/extractPAAC.Rd man/extractMDSScales.Rd man/AABLOSUM80.Rd man/extractScalesGap.Rd man/extractPSSMFeature.Rd man/extractCTDDClass.Rd man/AAEdgeAdj.Rd man/AAConn.Rd man/extractProtFP.Rd man/OptAA3d.Rd man/AAindex.Rd man/readFASTA.Rd man/extractAPAAC.Rd man/AARDF.Rd man/readPDB.Rd man/extractCTDT.Rd man/protseg.Rd man/extractPSSM.Rd man/extractCTDCClass.Rd man/AABLOSUM45.Rd man/extractSOCN.Rd man/acc.Rd man/AAPAM30.Rd man/extractMoran.Rd man/protr-package.Rd man/extractCTDTClass.Rd man/extractMoreauBroto.Rd man/AAWHIM.Rd man/AAGeom.Rd man/extractCTDD.Rd man/AAPAM70.Rd man/AAEigIdx.Rd man/AAPAM250.Rd man/AAMOE2D.Rd man/AA3DMoRSE.Rd man/AABLOSUM50.Rd man/AAMolProp.Rd man/AACPSA.Rd man/AAInfo.Rd man/extractCTriadClass.Rd man/AAPAM120.Rd man/twoSeqSim.Rd man/extractTC.Rd man/extractQSO.Rd man/extractFAScales.Rd man/extractCTriad.Rd man/protcheck.Rd man/AARandic.Rd man/twoGOSim.Rd man/AAGETAWAY.Rd man/extractProtFPGap.Rd man/extractCTDC.Rd man/AA2DACOR.Rd man/extractDC.Rd man/AAACF.Rd man/extractDescScales.Rd man/AAWalk.Rd man/AAMOE3D.Rd man/AAConst.Rd man/AATopo.Rd man/AAFGC.Rd man/AABLOSUM100.Rd man/extractAAC.Rd man/AAMetaInfo.Rd man/getUniProt.Rd man/extractScales.Rd man/AATopoChg.Rd
LICENSE

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.