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. 2005 Mar 9;219(3):555–565. doi: 10.1016/0022-2836(91)90193-A

Amino acid substitution matrices from an information theoretic perspective

Stephen F Altschul 1
PMCID: PMC7130686  PMID: 2051488

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 α1B-glycoprotein, the cystic fibrosis transmembrane conductance regulator and the globins.

Keywords: homology, sequence comparison, statistical significance, alignment algorithms, pattern recognition

Abbreviations: MSP, Maximal Segment Pair; Ig, immunoglobin

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