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.

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

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/pcm-01-extractScalesGap.R protr/R/desc-09-CTDD.R protr/R/misc-06-acc.R protr/R/desc-07-CTDCClass.R protr/R/misc-03-protcheck.R protr/R/pcm-04-extractFAScales.R protr/R/desc-07-CTDC.R protr/R/misc-01-readFASTA.R protr/R/desc-14-APAAC.R protr/R/desc-08-CTDTClass.R protr/R/pcm-05-extractMDSScales.R protr/R/desc-09-CTDDClass.R protr/R/desc-01-AAC.R protr/R/par-02-parGOSim.R protr/R/desc-06-Geary.R protr/R/misc-04-protseg.R protr/R/protr-package.R protr/R/pcm-01-extractScales.R protr/R/desc-13-PAAC.R protr/R/desc-15-PSSMFeature.R protr/R/pcm-03-extractProtFPGap.R protr/R/pcm-06-extractBLOSUM.R protr/R/pcm-02-extractDescScales.R protr/R/protr-datalist.R protr/R/desc-03-TC.R protr/R/desc-04-MoreauBroto.R protr/R/desc-12-QSO.R protr/R/desc-15-PSSM.R protr/R/desc-10-CTriadClass.R protr/R/desc-08-CTDT.R protr/R/misc-02-readPDB.R protr/R/desc-15-PSSMAcc.R protr/R/par-01-parSeqSim.R protr/R/desc-05-Moran.R protr/R/desc-02-DC.R protr/R/pcm-03-extractProtFP.R protr/R/desc-10-CTriad.R protr/R/misc-05-getUniProt.R protr/R/desc-11-SOCN.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

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