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Amino acid substitution matrices from protein blocks.

Proceedings of the National Academy of Sciences · 1992 · Vol. 89(22) · pp. 10915–10919

Steven Henikoff✉(Howard Hughes Medical Institute)Jorja G. Henikoff(Howard Hughes Medical Institute)

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.

Genomics and Phylogenetic Studies RNA and protein synthesis mechanisms Advanced Proteomics Techniques and ApplicationsSubstitution (logic)Amino acid substitutionAmino acidComputational biologySimilarity (geometry)Protein evolutionMatrix (chemical analysis)Sequence (biology)Sequence alignmentComputer science

MeSH terms

AlgorithmsAmino Acid SequenceAnimalsDrosophilaLod ScoreMathematicsMolecular Sequence DataProbabilityProteinsSoftwareCaenorhabditis elegansSequence Homology, Amino Acid

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