Format

Send to

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

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

Author information

1
Gene Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians Universität München, Munich, Germany.

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.

PMID:
22198341
DOI:
10.1038/nmeth.1818
[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for Nature Publishing Group
Loading ...
Support Center