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protr

Comprehensive toolkit for generating various numerical features of protein sequences described in Xiao et al. (2015) <DOI:10.1093/bioinformatics/btv042> (PDF).

Paper citation

Formatted citation:

Nan Xiao, Dong-Sheng Cao, Min-Feng Zhu, Qing-Song Xu (2015). protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences. Bioinformatics, 31(11), 1857–1859.

BibTeX entry:

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

Installation

To install protr from CRAN:

Or try the latest version on GitHub:

remotes::install_github("nanxstats/protr")

Browse the package vignette for a quick-start.

Shiny app

ProtrWeb, the Shiny web application built on protr, can be accessed from http://protr.org.

ProtrWeb is a user-friendly web application for computing the protein sequence descriptors (features) presented in the protr package.

List of supported descriptors

Commonly used descriptors

  • Amino acid composition descriptors

    • Amino acid composition
    • Dipeptide composition
    • Tripeptide composition

  • Autocorrelation descriptors

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

  • CTD descriptors

    • Composition
    • Transition
    • Distribution

  • Conjoint Triad descriptors

  • Quasi-sequence-order descriptors

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

  • Pseudo amino acid composition (PseAAC)

    • Pseudo amino acid composition
    • Amphiphilic pseudo amino acid composition

  • Profile-based descriptors

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

Proteochemometric (PCM) modeling descriptors

  • 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

Similarity computation

Local and global pairwise sequence alignment for protein sequences:

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

Miscellaneous tools and datasets

  • 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

Contribute

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that the protr project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.