A Site- and Time-Heterogeneous Model of Amino Acid Replacement
نویسندگان
چکیده
منابع مشابه
A site- and time-heterogeneous model of amino acid replacement.
We combined the category (CAT) mixture model (Lartillot N, Philippe H. 2004) and the nonstationary break point (BP) model (Blanquart S, Lartillot N. 2006) into a new model, CAT-BP, accounting for variations of the evolutionary process both along the sequence and across lineages. As in CAT, the model implements a mixture of distinct Markovian processes of substitution distributed among sites, th...
متن کاملRunning head : Site - and time - heterogeneous model of evolution A site - and time - heterogeneous model of amino - acid replace - ment
We combined the CAT mixture model (Lartillot and Philippe 2004) and the non-stationary BP model (Blanquart and Lartillot 2006) into a new model, CAT-BP, accounting for variations of the evolutionary process both along the sequence and across lineages. As in CAT, the model implements a mixture of distinct Markovian processes of substitution distributed among sites, thus accommodating site-specif...
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MOTIVATION The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. This model assumes that every location on the protein sequence has the same background distribution of amino acids, an assumption that is incompatible with the observed heterogeneity of protein amino acid profiles and with the suc...
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Most current models of sequence evolution assume that all sites of a protein evolve under the same substitution process, characterized by a 20 x 20 substitution matrix. Here, we propose to relax this assumption by developing a Bayesian mixture model that allows the amino-acid replacement pattern at different sites of a protein alignment to be described by distinct substitution processes. Our mo...
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A statistical approach was applied to select those models that best fit each individual mitochondrial (mt) protein at different taxonomic levels of metazoans. The existing mitochondrial replacement matrices, MtREV and MtMam, were found to be the best-fit models for the mt-proteins of vertebrates, with the exception of Nd6, at different taxonomic levels. Remarkably, existing mitochondrial matric...
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ژورنال
عنوان ژورنال: Molecular Biology and Evolution
سال: 2008
ISSN: 1537-1719,0737-4038
DOI: 10.1093/molbev/msn018