Evolutionary footprint of coevolving positions in genes.

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Serval ID
serval:BIB_EA95317606C6
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Evolutionary footprint of coevolving positions in genes.
Journal
Bioinformatics
Author(s)
Dib L., Silvestro D., Salamin N.
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Publication state
Published
Issued date
2014
Volume
30
Number
9
Pages
1241-1249
Language
english
Abstract
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
Yes
Create date
23/06/2014 9:44
Last modification date
25/09/2019 7:11
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