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Mol Biol Evol. 1996 Dec;13(10):1368-74.

Modeling residue usage in aligned protein sequences via maximum likelihood.

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  • Los Alamos National Laboratory, New Mexico 87545, USA. billb@lanl.gov


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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