title: Amino acid substitution matrices from an information theoretic perspective.
abstract: Protein sequence alignments have become an important tool for molecular biologists. Local alignments are frequently constructed with the aid of a "substitution score matrix" that specifies a score for aligning each pair of amino acid residues. Over the years, many different substitution matrices have been proposed, based on a wide variety of rationales. Statistical results, however, demonstrate that any such matrix is implicitly a "log-odds" matrix, with a specific target distribution for aligned pairs of amino acid residues. In the light of information theory, it is possible to express the scores of a substitution matrix in bits and to see that different matrices are better adapted to different purposes. The most widely used matrix for protein sequence comparison has been the PAM-250 matrix. It is argued that for database searches the PAM-120 matrix generally is more appropriate, while for comparing two specific proteins with suspected homology the PAM-200 matrix is indicated. Examples discussed include the lipocalins, human alpha 1 B-glycoprotein, the cystic fibrosis transmembrane conductance regulator and the globins.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894.
authors.forename: S F
authors.initials: SF
authors.lastname: Altschul
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D015233:Models, Statistical; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D013816:Thermodynamics
chemical_list: D011506:Proteins