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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.
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L. Steven Johnson
Sean R. Eddy
Elon Portugaly
BMC Bioinformatics
SHILAP Revista de lepidopterología
Howard Hughes Medical Institute
Washington University in St. Louis
Hebrew University of Jerusalem
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Johnson et al. (Wed,) studied this question.
www.synapsesocial.com/papers/69da0fa1ba6014a02e835835 — DOI: https://doi.org/10.1186/1471-2105-11-431
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