Literature DB >> 1438297

Amino acid substitution matrices from protein blocks.

S Henikoff1, J G Henikoff.   

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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Year:  1992        PMID： 1438297      PMCID： PMC50453          DOI： 10.1073/pnas.89.22.10915

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  23 in total

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Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
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2.  The SWISS-PROT protein sequence data bank.

Authors:  A Bairoch; B Boeckmann
Journal:  Nucleic Acids Res       Date:  1991-04-25       Impact factor: 16.971

3.  Automatic generation of primary sequence patterns from sets of related protein sequences.

Authors:  R F Smith; T F Smith
Journal:  Proc Natl Acad Sci U S A       Date:  1990-01       Impact factor: 11.205

4.  Multiple sequence alignment with hierarchical clustering.

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5.  Searching through sequence databases.

Authors:  R F Doolittle
Journal:  Methods Enzymol       Date:  1990       Impact factor: 1.600

6.  Mutation data matrix and its uses.

Authors:  D G George; W C Barker; L T Hunt
Journal:  Methods Enzymol       Date:  1990       Impact factor: 1.600

7.  Finding protein similarities with nucleotide sequence databases.

Authors:  S Henikoff; J C Wallace; J P Brown
Journal:  Methods Enzymol       Date:  1990       Impact factor: 1.600

8.  A tool for multiple sequence alignment.

Authors:  D J Lipman; S F Altschul; J D Kececioglu
Journal:  Proc Natl Acad Sci U S A       Date:  1989-06       Impact factor: 11.205

9.  Amino acid substitutions in structurally related proteins. A pattern recognition approach. Determination of a new and efficient scoring matrix.

Authors:  J L Risler; M O Delorme; H Delacroix; A Henaut
Journal:  J Mol Biol       Date:  1988-12-20       Impact factor: 5.469

10.  Amino acid substitution matrices from an information theoretic perspective.

Authors:  S F Altschul
Journal:  J Mol Biol       Date:  1991-06-05       Impact factor: 5.469
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