CAPS: coevolution analysis using protein sequences

Mario A Fares; David McNally

doi:10.1093/bioinformatics/btl493

CAPS: coevolution analysis using protein sequences

Bioinformatics. 2006 Nov 15;22(22):2821-2. doi: 10.1093/bioinformatics/btl493. Epub 2006 Sep 27.

Authors

Mario A Fares¹, David McNally

Affiliation

¹ Evolutionary Genetics and Bioinformatics Laboratory, Department of Genetics Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Dublin, Ireland. faresm@tcd.ie

PMID: 17005535
DOI: 10.1093/bioinformatics/btl493

Abstract

Coevolution Analysis using Protein Sequences (CAPS) is a PERL based software that identifies co-evolution between amino acid sites. Blosum-corrected amino acid distances are used to identify amino acid co-variation. The phylogenetic sequence relationships are used to remove the phylogenetic and stochastic dependencies between sites. The 3D protein structure is used to identify the nature of the dependencies between co-evolving amino acid sites. Friendly interpretable output files are generated.

Availability: CAPS version 1 is available at http://bioinf.gen.tcd.ie/~faresm/software/caps/. Distribution versions for Linux/Unix, Mac OS X and Windows operating systems are available, including manual and example files.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Cluster Analysis
Computational Biology / methods*
Computer Graphics
Evolution, Molecular
Internet
Phylogeny
Programming Languages
Proteins / chemistry*
Proteomics / methods
Sequence Analysis, Protein
Software
User-Computer Interface

Substances

Proteins