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. 2011 Dec 25;9(2):173-5.
doi: 10.1038/nmeth.1818.

HHblits: Lightning-Fast Iterative Protein Sequence Searching by HMM-HMM Alignment

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HHblits: Lightning-Fast Iterative Protein Sequence Searching by HMM-HMM Alignment

Michael Remmert et al. Nat Methods. .

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.

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