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PMID: 1438297 Published · ppublish English Comparative Study Journal Article Research Support, U.S. Gov't, P.H.S.

Amino acid substitution matrices from protein blocks.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 89 ·No. 22 ·1992-11-15 ·Pages 10915-9

Henikoff S, Henikoff JG

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.

MeSH Terms
Algorithms Amino Acid Sequence Animals Caenorhabditis elegans/genetics Drosophila/genetics Lod Score Mathematics Molecular Sequence Data Probability Proteins/chemistry,genetics Sequence Homology, Amino Acid Software
Chemicals
Proteins
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Henikoff S
Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98104.
Henikoff J G
References (23)
23 references, click to expand
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.89.22.10915
Published
1992-11-15
Pages
10915-9
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC50453
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.89.22.10915 PMC Full Text View journal details
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