Molecular Biology and Evolution, Vol 13, 1368-1374, Copyright © 1996 by Society for Molecular Biology and Evolution
WJ Bruno
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.
ORIGINAL ARTICLE
Modeling residue usage in aligned protein sequences via maximum likelihood
Los Alamos National Laboratory, New Mexico 87545, USA. billb@lanl.gov
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