An Alternative Model of Amino Acid Replacement

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dc.creatorCrooks, Gavin E.
dc.creatorBrenner, Steven E.
dc.date2004-07-24
dc.date2004-10-25
dc.date.accessioned2026-07-07T05:58:34Z
dc.date.available2026-07-07T05:58:34Z
dc.descriptionThe observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. This model assumes that every location on the protein sequence has the same background distribution of amino acids, an assumption that is incompatible with the observed heterogeneity of protein amino acid profiles and with the success of profile multiple sequence alignment. We propose an alternative model of amino acid replacement during protein evolution based upon the assumption that the variation of the amino acid background distribution from one residue to the next is sufficient to explain the observed sequence correlations of homologs. The resulting dynamical model of independent replacements drawn from heterogeneous backgrounds is simple and consistent, and provides a unified homology match score for sequence-sequence, sequence-profile and profile-profile alignment.
dc.descriptionMinor improvements. Added figure and references
dc.identifierhttps://arxiv.org/abs/q-bio/0407032
dc.identifierhttp://arxiv.org/abs/q-bio/0407032
dc.identifierBioinformatics 2005 21(7):975-980
dc.identifierdoi:10.1093/bioinformatics/bti109
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/88403
dc.subjectBiomolecules
dc.subjectPopulations and Evolution
dc.titleAn Alternative Model of Amino Acid Replacement
dc.typetext

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