Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915-9.

Amino acid substitution matrices from protein blocks.

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Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98104.

Abstract

Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins. This led to marked improvements in alignments and in searches using queries from each of the groups.

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PMCID:: PMC50453

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