Comprehensive toolkit for generating various numerical representation schemes of protein sequence. The descriptors included in the protr package are extensively utilized in bioinformatics and chemogenomics.

• Amino acid composition

  • Amino acid composition
  • Dipeptide composition
  • Tripeptide composition

• Autocorrelation

  • Normalized Moreau-Broto autocorrelation
  • Moran autocorrelation
  • Geary autocorrelation

• CTD

  • Composition
  • Transition
  • Distribution

• Conjoint Triad

• Quasi-sequence-order descriptors

  • Sequence-order-coupling number
  • Quasi-sequence-order descriptors

• Pseudo amino acid composition

  • Pseudo amino acid composition
  • Amphiphilic pseudo amino acid composition

• Profile-based descriptors

  • Profile-based descriptors derived by PSSM (Position-Specific Scoring Matrix)

• Scales-based descriptors derived by principal components analysis
  • Scales-based descriptors derived by amino acid properties (AAindex)
  • Scales-based descriptors derived by 20+ classes of 2D and 3D molecular descriptors (Topological, WHIM, VHSE, etc.)
• Scales-based descriptors derived by factor analysis
• Scales-based descriptors derived by multidimensional scaling
• BLOSUM and PAM matrix-derived descriptors

Local and global pairwise sequence alignment for protein sequences:

• Between two protein sequences
• Parallelized pairwise similarity calculation with a list of protein sequences

GO semantic similarity measures:

• Between two groups of GO terms / two Entrez Gene IDs
• Parallelized pairwise similarity calculation with a list of GO terms / Entrez Gene IDs

• Retrieve protein sequences from UniProt
• Read protein sequences in FASTA format
• Read protein sequences in PDB format
• Sanity check of the amino acid types appeared in the protein sequences
• Protein sequence segmentation
• Auto cross covariance (ACC) for generating scales-based descriptors of the same length
• 20+ pre-computed 2D and 3D descriptor sets for the 20 amino acids to use with the scales-based descriptors
• BLOSUM and PAM matrices for the 20 amino acids
• Meta information of the 20 amino acids

ProtrWeb, the web server built on protr, is located at:

http://protr.org

ProtrWeb does not require any knowledge of R programming for the users, it is a user-friendly and one-click-to-go online platform for computing the descriptors presented in the protr package.

Formatted citation:

Nan Xiao, Dong-Sheng Cao, Min-Feng Zhu, and Qing-Song Xu. (2015). protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences. Bioinformatics 31, 1857-1859.

BibTeX entry:

@article{Xiao2015,
author = {Xiao, Nan and Cao, Dong-Sheng and Zhu, Min-Feng and Xu, Qing-Song.},
doi = {10.1093/bioinformatics/btv042},
issn = {1367-4803},
journal = {Bioinformatics},
number = {11},
pages = {1857--1859},
title = {{protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btv042},
volume = {31},
year = {2015}
}

• CRAN: https://cran.r-project.org/package=protr
• GitHub: https://github.com/road2stat/protr
• Bug report: https://github.com/road2stat/protr/issues