An alternative model of amino acid replacement | Zendy

Gavin E. Crooks | Zendy; Steven E. Brenner | Zendy

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An alternative model of amino acid replacement

Author(s) -

Gavin E. Crooks,

Steven E. Brenner

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bti109

Subject(s) - sequence (biology) , protein superfamily , amino acid , homology (biology) , peptide sequence , sequence logo , protein evolution , sequence alignment , computational biology , protein sequencing , amino acid residue , amino acid substitution , homology modeling , multiple sequence alignment , biology , genetics , biochemistry , mutation , gene , enzyme

The 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.

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