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- Title
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
- Authors
Remmert, Michael; Biegert, Andreas; Hauser, Andreas; Söding, Johannes
- Abstract
Sequence-based protein function and structure prediction depends crucially on sequence-search sensitivity and accuracy of the resulting sequence alignments. We present an open-source, general-purpose tool that represents both query and database sequences by profile hidden Markov models (HMMs): 'HMM-HMM-based lightning-fast iterative sequence search' (HHblits; http://toolkit.genzentrum.lmu.de/hhblits/). Compared to the sequence-search tool PSI-BLAST, HHblits is faster owing to its discretized-profile prefilter, has 50-100% higher sensitivity and generates more accurate alignments.
- Subjects
GENOMICS; MARKOV processes; AMINO acid sequence; ITERATIVE methods (Mathematics); STOCHASTIC sequences
- Publication
Nature Methods, 2012, Vol 9, Issue 2, p173
- ISSN
1548-7091
- Publication type
Article
- DOI
10.1038/nmeth.1818