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

Remmert, M.; Biegert, A.; Hauser, A.; Söding, J.

doi:10.1038/NMETH.1818

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

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Söding, J.
Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Citation

Remmert, M., Biegert, A., Hauser, A., & Söding, J. (2012). HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature Methods, 9(2), 173-175. doi:10.1038/NMETH.1818.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0015-8D56-A

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.