title: Modeling residue usage in aligned protein sequences via maximum likelihood.
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.
authors.affiliation: Los Alamos National Laboratory, New Mexico 87545, USA. billb@lanl.gov
authors.forename: W J
authors.initials: WJ
authors.lastname: Bruno
mesh_terms: D000596:Amino Acids / Q000235:genetics*; D003198:Computer Simulation; D016013:Likelihood Functions; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D000596:Amino Acids