HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
basic_science · Level V
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- Record sourced from PubMed, PMID 22198341.
- Also identified by DOI 10.1038/nmeth.1818.
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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.
Medical subject headings
- Proteins
- Sequence Alignment