Modeling residue usage in aligned protein sequences via maximum likelihood

A computational method is presented for characterizing residue usage, i.e., site-specific residue frequencies, in aligned protein sequences. The method obtains frequency estimates that maximize the likelihood of the sequences in a simple model for sequence evolution, given a tree or a set of candida...

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Veröffentlicht in:	Molecular biology and evolution 1996-12, Vol.13 (10), p.1368-1374
1. Verfasser:	Bruno, W J
Format:	Artikel
Sprache:	eng
Schlagworte:	Amino Acids - genetics Computer Simulation Likelihood Functions Phylogeny Sequence Alignment - methods
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container_title	Molecular biology and evolution
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creator	Bruno, W J
description	A computational method is presented for characterizing residue usage, i.e., site-specific residue frequencies, in aligned protein sequences. The method obtains frequency estimates that maximize the likelihood of the sequences in a simple model for sequence evolution, given a tree or a set of candidate trees computed by other methods. These maximum-likelihood frequencies constitute a profile of the sequences, and thus the method offers a rigorous alternative to sequence weighting for constructing such a profile. The ability of this method to discard misleading phylogenetic effects allows the biochemical propensities of different positions in a sequence to be more clearly observed and interpreted.
doi_str_mv	10.1093/oxfordjournals.molbev.a025583
format	Article
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subjects	Amino Acids - genetics Computer Simulation Likelihood Functions Phylogeny Sequence Alignment - methods
title	Modeling residue usage in aligned protein sequences via maximum likelihood
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