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PubMed · 8014990

Detecting patterns in protein sequences.

A F Neuwald·P Green
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Abstract

The detection of conserved sequence patterns (motifs) in related proteins often yields valuable structural and functional insights. We describe a method that utilizes rigorous statistics and a depth-first search procedure to efficiently and exhaustively search a set of proteins for significant patterns up to a specified length. Additional procedures classify related patterns into groups and identify protein segments most likely to share a common motif. The utility of the method was demonstrated on several difficult test problems; detection of motifs among 56 proteins in the acyltransferase family, detection of a dinucleotide-binding fold present within a small subset of a set of 91 distantly related and unrelated proteins, detection of the helix-turn-helix motif in 15 distantly related proteins and detection of subtle internal repeats in a prenyltransferase. In a search of a large set of sequences for internal repeats, the method detected novel ankyrin-like repeats in an Escherichia coli protein.

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AcetyltransferasesAlgorithmsAmino Acid SequenceConserved SequenceMolecular Sequence DataPattern Recognition, AutomatedSequence AlignmentStatistics as TopicJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

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A F Neuwald, P Green. 1994-06-24. Detecting patterns in protein sequences.. https://doi.org/10.1006/jmbi.1994.1407

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