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Amino acid substitution matrices from protein blocks.
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
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Cited by over 100 PubMed Central articles
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Databases of homologous gene families for comparative genomics.
Penel S, Arigon AM, Dufayard JF, Sertier AS, Daubin V, Duret L, Gouy M, Perrière G.
BMC Bioinformatics. 2009 Jun 16; 10 Suppl 6:S3. Epub 2009 Jun 16.
[BMC Bioinformatics. 2009]
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Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements.
Creanza TM, Horner DS, D'Addabbo A, Maglietta R, Mignone F, Ancona N, Pesole G.
BMC Bioinformatics. 2009 Jun 16; 10 Suppl 6:S2. Epub 2009 Jun 16.
[BMC Bioinformatics. 2009]
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Prediction of type III secretion signals in genomes of gram-negative bacteria.
Löwer M, Schneider G.
PLoS One. 2009 Jun 15; 4(6):e5917. Epub 2009 Jun 15.
[PLoS One. 2009]
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