Modeling residue usage in aligned protein sequences via maximum likelihood.

W J Bruno

doi:10.1093/oxfordjournals.molbev.a025583

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PubMed · 8952081

Modeling residue usage in aligned protein sequences via maximum likelihood.

W J Bruno

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Abstract

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.

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Amino Acids Computer Simulation Likelihood Functions Phylogeny Sequence Alignment Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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W J Bruno. 1996. Modeling residue usage in aligned protein sequences via maximum likelihood.. https://doi.org/10.1093/oxfordjournals.molbev.a025583

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