HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.

Remmert M; Biegert A; Hauser A; Söding J

doi:10.1038/nmeth.1818

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.

Affiliations

1. Gene Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians Universität München, Munich, Germany.
Authors
Remmert M¹
(1 author)

ORCIDs linked to this article

Nature Methods, 25 Dec 2011, 9(2):173-175
https://doi.org/10.1038/nmeth.1818 PMID: 22198341

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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