Abstract
Our search heuristic, HMMERHEAD, significantly reduces the time needed to score a profile-HMM against large sequence databases. This search heuristic allowed us to implement an iterative profile-HMM search method, JackHMMER, which detects significantly more remote protein homologs than SAM's T2K and NCBI's PSI-BLAST.
Keywords
Hidden Markov modelViterbi algorithmComputer scienceBeam searchHeuristicBenchmark (surveying)Search algorithmPattern recognition (psychology)Database search engineArtificial intelligenceMarkov chainMachine learningAlgorithmSpeech recognitionSearch engineInformation retrieval
MeSH Terms
AlgorithmsArtificial IntelligenceBase SequenceDatabasesProteinMarkov ChainsProteinsSequence AlignmentSoftware
Affiliated Institutions
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Publication Info
- Year
- 2010
- Type
- article
- Volume
- 11
- Issue
- 1
- Pages
- 431-431
- Citations
- 1392
- Access
- Closed
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Cite This
L. Steven Johnson,
Sean R. Eddy,
Elon Portugaly
(2010).
Hidden Markov model speed heuristic and iterative HMM search procedure.
BMC Bioinformatics
, 11
(1)
, 431-431.
https://doi.org/10.1186/1471-2105-11-431
Identifiers
- DOI
- 10.1186/1471-2105-11-431
- PMID
- 20718988
- PMCID
- PMC2931519