Amino acid substitution matrices from protein bloc...[Proc Natl Acad Sci U S A. 1992]

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

Amino acid substitution matrices from protein blocks.

Henikoff S, Henikoff JG.

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

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.

PMID: 1438297 [PubMed - indexed for MEDLINE]

PMCID: PMC50453

Amino acid substitution matrices from an information theoretic perspective. [J Mol Biol. 1991]
Effective protein sequence comparison. [Methods Enzymol. 1996]
A transition probability model for amino acid substitutions from blocks. [J Comput Biol. 2003]
Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. [Bioinformatics. 2000]
Optimizing substitution matrices by separating score distributions. [Bioinformatics. 2004]
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Amino acid substitution matrices from protein blocks.

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