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Designing Patterns and Profiles for Faster HMM Search by Yanni Sun; J. Buhler is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is Designing Patterns and Profiles for Faster HMM Search about?

Profile HMMs are powerful tools for modeling conserved motifs in proteins. They are widely used by search tools to classify new protein sequences into families based on domain architecture. However, the proliferation of known motifs and new proteomic sequence data poses a computational challenge for search, requiring days of CPU time to annotate an organism's proteome. It is highly desirable to speed up HMM search in large databases. We design PROSITE-like patterns and short profiles that are used as filters to rapidly eliminate protein-motif pairs for which a full profile HMM comparison does not yield a significant match. The design of the pattern-based filters is formulated as a multichoice knapsack problem. Profile-based filters with high sensitivity are extracted from a profile HMM based on their theoretical sensitivity and false positive rate. Experiments show that our profile-based filters achieve high sensitivity (near 100 percent) while keeping around 20Â speedup with respect to the unfiltered search program. Pattern-based filters typically retain at least 90 percent of the sensitivity of the source HMM with 30-40Â speedup. The profile-based filters have sensitivity compara

Who reads Designing Patterns and Profiles for Faster HMM Search?

Author

Yanni Sun; J. Buhler

Publisher

Institute of Electrical and Electronics Engineers (IEEE)

Published

2009

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)