Evolutionary footprint of coevolving positions in genes.

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ID Serval
serval:BIB_EA95317606C6
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
Evolutionary footprint of coevolving positions in genes.
Périodique
Bioinformatics
Auteur⸱e⸱s
Dib L., Silvestro D., Salamin N.
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Statut éditorial
Publié
Date de publication
2014
Volume
30
Numéro
9
Pages
1241-1249
Langue
anglais
Résumé
MOTIVATION: The analysis of molecular coevolution provides information on the potential functional and structural implication of positions along DNA sequences, and several methods are available to identify coevolving positions using probabilistic or combinatorial approaches. The specific nucleotide or amino acid profile associated with the coevolution process is, however, not estimated, but only known profiles, such as the Watson-Crick constraint, are usually considered a priori in current measures of coevolution.
RESULTS: Here, we propose a new probabilistic model, Coev, to identify coevolving positions and their associated profile in DNA sequences while incorporating the underlying phylogenetic relationships. The process of coevolution is modeled by a 16 × 16 instantaneous rate matrix that includes rates of transition as well as a profile of coevolution. We used simulated, empirical and illustrative data to evaluate our model and to compare it with a model of 'independent' evolution using Akaike Information Criterion. We showed that the Coev model is able to discriminate between coevolving and non-coevolving positions and provides better specificity and specificity than other available approaches. We further demonstrate that the identification of the profile of coevolution can shed new light on the process of dependent substitution during lineage evolution.
Pubmed
Web of science
Open Access
Oui
Création de la notice
23/06/2014 8:44
Dernière modification de la notice
14/02/2022 7:57
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