title: HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
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.
authors.affiliation: Gene Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians Universität München, Munich, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Remmert
authors.forename: Andreas
authors.initials: A
authors.lastname: Biegert
authors.forename: Andreas
authors.initials: A
authors.lastname: Hauser
authors.forename: Johannes
authors.initials: J
authors.lastname: Söding
mesh_terms: D008390:Markov Chains; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment
chemical_list: D011506:Proteins