CAPS: coevolution analysis using protein sequences
- PMID: 17005535
- DOI: 10.1093/bioinformatics/btl493
CAPS: coevolution analysis using protein sequences
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.
Similar articles
-
MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.BMC Bioinformatics. 2005 Mar 22;6:64. doi: 10.1186/1471-2105-6-64. BMC Bioinformatics. 2005. PMID: 15780146 Free PMC article.
-
ET viewer: an application for predicting and visualizing functional sites in protein structures.Bioinformatics. 2006 Aug 15;22(16):2049-50. doi: 10.1093/bioinformatics/btl285. Epub 2006 Jun 29. Bioinformatics. 2006. PMID: 16809388
-
DEPD: a novel database for differentially expressed proteins.Bioinformatics. 2005 Sep 15;21(18):3694-6. doi: 10.1093/bioinformatics/bti580. Epub 2005 Jul 14. Bioinformatics. 2005. PMID: 16020467
-
Unix survival guide.Curr Protoc Bioinformatics. 2007 Jan;Appendix 1:Appendix 1C. doi: 10.1002/0471250953.bia01cs16. Curr Protoc Bioinformatics. 2007. PMID: 18428775 Review.
-
X Window System survival guide.Curr Protoc Bioinformatics. 2007 Mar;Appendix 1:Appendix 1D. doi: 10.1002/0471250953.bia01ds17. Curr Protoc Bioinformatics. 2007. PMID: 18428776 Review.
Cited by
-
Genome-Wide Analysis of Wheat GATA Transcription Factor Genes Reveals Their Molecular Evolutionary Characteristics and Involvement in Salt and Drought Tolerance.Int J Mol Sci. 2022 Dec 20;24(1):27. doi: 10.3390/ijms24010027. Int J Mol Sci. 2022. PMID: 36613470 Free PMC article.
-
Coevolution analysis of amino-acids reveals diversified drug-resistance solutions in viral sequences: a case study of hepatitis B virus.Virus Evol. 2020 Feb 6;6(1):veaa006. doi: 10.1093/ve/veaa006. eCollection 2020 Jan. Virus Evol. 2020. PMID: 32158552 Free PMC article.
-
Why should we care about molecular coevolution?Evol Bioinform Online. 2008 Feb 14;4:29-38. Evol Bioinform Online. 2008. PMID: 19204805 Free PMC article.
-
Molecular Characterization of the Coat Protein Gene of Greek Apple Stem Pitting Virus Isolates: Evolution through Deletions, Insertions, and Recombination Events.Plants (Basel). 2021 May 3;10(5):917. doi: 10.3390/plants10050917. Plants (Basel). 2021. PMID: 34063623 Free PMC article.
-
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.Chem Rev. 2016 Jun 8;116(11):6370-90. doi: 10.1021/acs.chemrev.5b00631. Epub 2016 Apr 13. Chem Rev. 2016. PMID: 27074285 Free PMC article. Review.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Miscellaneous
