Literature DB >> 17005535

CAPS: coevolution analysis using protein sequences.

Mario A Fares1, David McNally.   

Abstract

UNLABELLED: 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.

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Year:  2006        PMID： 17005535     DOI： 10.1093/bioinformatics/btl493

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  57 in total

1.  Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation.

Authors:  Jonathan Corbi; Julien Y Dutheil; Catherine Damerval; Maud I Tenaillon; Domenica Manicacci
Journal:  Ann Bot       Date:  2012-02-02       Impact factor: 4.357

2.  A Comprehensive Study of Molecular Evolution at the Self-Incompatibility Locus of Rosaceae.

Authors:  Jahanshah Ashkani; D J G Rees
Journal:  J Mol Evol       Date:  2015-12-29       Impact factor: 2.395

Review 3.  Applying evolutionary genetics to developmental toxicology and risk assessment.

Authors:  Maxwell C K Leung; Andrew C Procter; Jared V Goldstone; Jonathan Foox; Robert DeSalle; Carolyn J Mattingly; Mark E Siddall; Alicia R Timme-Laragy
Journal:  Reprod Toxicol       Date:  2017-03-04       Impact factor: 3.143

4.  Rapid molecular evolution across amniotes of the IIS/TOR network.

Authors:  Suzanne E McGaugh; Anne M Bronikowski; Chih-Horng Kuo; Dawn M Reding; Elizabeth A Addis; Lex E Flagel; Fredric J Janzen; Tonia S Schwartz
Journal:  Proc Natl Acad Sci U S A       Date:  2015-05-19       Impact factor: 11.205

5.  Negative purifying selection drives prion and doppel protein evolution.

Authors:  Kyriakos Tsangaras; Sergios-Orestis Kolokotronis; Rainer G Ulrich; Serge Morand; Johan Michaux; Alex D Greenwood
Journal:  J Mol Evol       Date:  2014-07-20       Impact factor: 2.395

6.  Molecular Evolution of rbcL in Orthotrichales (Bryophyta): Site Variation, Adaptive Evolution, and Coevolutionary Patterns of Amino Acid Replacements.

Authors:  Moisès Bernabeu; Josep A Rosselló
Journal:  J Mol Evol       Date:  2021-02-20       Impact factor: 2.395

7.  Two frequenins in Drosophila: unveiling the evolutionary history of an unusual neuronal calcium sensor (NCS) duplication.

Authors:  Alejandro Sánchez-Gracia; Jesús Romero-Pozuelo; Alberto Ferrús
Journal:  BMC Evol Biol       Date:  2010-02-19       Impact factor: 3.260

8.  Mutational dynamics of murine angiogenin duplicates.

Authors:  Francisco M Codoñer; Silvia Alfonso-Loeches; Mario A Fares
Journal:  BMC Evol Biol       Date:  2010-10-15       Impact factor: 3.260

9.  Molecular Characterization of the Coat Protein Gene of Greek Apple Stem Pitting Virus Isolates: Evolution through Deletions, Insertions, and Recombination Events.

Authors:  Matthaios M Mathioudakis; Varvara I Maliogka; Thierry Candresse; Osmar Nickel; Thor Vinicius Martins Fajardo; Daria Budzyńska; Beata Hasiów-Jaroszewska; Nikolaos I Katis
Journal:  Plants (Basel)       Date:  2021-05-03

Review 10.  Applications of Deep Mutational Scanning in Virology.

Authors:  Thomas D Burton; Nicholas S Eyre
Journal:  Viruses       Date:  2021-05-28       Impact factor: 5.048
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