README.md

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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, and 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},
  issn = {1367-4803},
  url = {http://bioinformatics.oxfordjournals.org/content/31/11/1857}
}

Installation

To install protr from CRAN:

install.packages("protr")

Or try the latest version on GitHub:

# install.packages("devtools")
devtools::install_github("road2stat/protr")

Browse the package vignette for a quick-start.

Shiny Web Application

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.

Descriptors List

Commonly used descriptors

Proteochemometric (PCM) modeling descriptors

Similarity Computation

Local and global pairwise sequence alignment for protein sequences:

GO semantic similarity measures:

Miscellaneous tools and datasets

Links

Contribute

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



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protr documentation built on Nov. 18, 2017, 9:03 a.m.