CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions-Reference-Cited by-同舟云学术

CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions

Published:2023-10-01 Issue:10 Volume:39 Page:
ISSN:1367-4811
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Barteri Fabio¹²^ORCID,Valenzuela Alejandro¹²,Farré Xavier³^ORCID,de Juan David¹^ORCID,Muntané Gerard¹⁴⁵,Esteve-Altava Borja⁶,Navarro Arcadi¹²⁷⁸

Affiliation:

1. IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra . C. Doctor Aiguader 88 , Barcelona 08003, Spain

2. BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation , C/ Wellington 30 , Barcelona 08006, Spain

3. Genomes for Life-GCAT Lab, GermanTrias i Pujol Research Institute (IGTP) , Camí de les Escoles, s/n , Badalona 08916, Spain

4. Institut d’Investigació Sanitària Pere Virgili (IISPV), Hospital Universitari Institut Pere Mata, Universitat Rovira i Virgili . Avda. Josep Laporte, 2 – Planta 0 – E2 color taronja , Reus 43204, Spain

5. Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM) , Av. Monforte de Lemos, 3-5. Pabellón 11. Planta 0 . Madrid 28029, Spain

6. European Molecular Biology Laboratory , Meyerhofstraße 1 , Heidelberg 69117, Germany

7. Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra , Pg. Lluís Companys 23 , Barcelona 08010, Spain

8. Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , C. Doctor Aiguader N88 , Barcelona 08003, Spain

Abstract

Abstract Motivation Coincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their phylogenetic context. Such findings can provide useful insights into the genetic architecture of complex phenotypes. Results Here we introduce CAAStools, a set of bioinformatics tools to identify and validate CAAS in orthologous protein alignments for predefined groups of species representing the phenotypic values targeted by the user. Availability and implementation CAAStools source code is available at http://github.com/linudz/caastools, along with documentation and examples.

Funder

Departament de Recerca i Universitats de la Generalitat de Catalunya

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad623/52188222/btad623.pdf

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