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Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1992 Nov 15;89(22):10915–10919. doi: 10.1073/pnas.89.22.10915

Amino acid substitution matrices from protein blocks.

S Henikoff 1, J G Henikoff 1
PMCID: PMC50453  PMID: 1438297

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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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

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