article Open AccessTop 10% cited
Hidden Markov model speed heuristic and iterative HMM search procedure
BMC Bioinformatics · 2010 · Vol. 11(1) · pp. 431–431
L. Steven Johnson✉(Washington University in St. Louis)Sean R. Eddy(Janelia Research Campus)Elon Portugaly(Hebrew University of Jerusalem)
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.
Genomics and Phylogenetic StudiesAdvanced Proteomics Techniques and ApplicationsProtein Structure and DynamicsHidden Markov modelViterbi algorithmComputer scienceBeam searchHeuristicBenchmark (surveying)Search algorithmPattern recognition (psychology)Database search engineArtificial intelligence
MeSH terms
AlgorithmsArtificial IntelligenceBase SequenceMarkov ChainsProteinsSoftwareSequence AlignmentDatabases, Protein
Funding
- Howard Hughes Medical Institute
- Washington University in St. Louis
- National Institutes of Health
- Leibniz-Gemeinschaft
Citations
1,475
FWCI
10.01
field-weighted impact
References
17
Percentile
99%
vs. same field & year
Citations per year
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References
Basic local alignment search tool
Journal of Molecular Biology · 1990 · 93,570 citations
The Pfam Protein Families Database
Nucleic Acids Research · 2002 · 14,220 citations
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Nucleic Acids Research · 1997 · 74,154 citations
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