Amino acid substitution matrices from protein blocks.

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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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Journal

Journal ID (iso-abbrev): Proc Natl Acad Sci U S A

Title: Proceedings of the National Academy of Sciences of the United States of America

Publisher: Proceedings of the National Academy of Sciences

ISSN: 0027-8424

ISSN (Print): 0027-8424

Publication date (Electronic): Nov 15 1992

Volume: 89

Issue: 22

Affiliations

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

Article

DOI: 10.1073/pnas.89.22.10915

PMC ID: 50453

PubMed ID: 1438297

SO-VID: f7a9b73d-0d37-41a1-bc2a-cacd1743a982

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