HH-suite3 for fast remote homology detection and deep protein annotation

• Published in: BMC bioinformatics Vol. 20; no. 1; pp. 473 - 15
• Main Authors: Steinegger, Martin, Meier, Markus, Mirdita, Milot, Vöhringer, Harald, Haunsberger, Stephan J., Söding, Johannes
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 14.09.2019; BioMed Central; BMC
• Subjects: Algorithm; Algorithms; Alignment; Amino acid sequence; Amino acid sequencing; Annotations; Computer programs; Explosions; Freeware; Genomics; Homology; Homology (Biology); Homology detection; Markov chains; Markov processes; Message passing; Methods; Observations; Open source software; Parallel processing; Profile HMM; Protein alignment; Protein folding; Protein structure; Proteins; Searching; Sequence search; SIMD; Software; Software packages; Source code; Structure-function relationships; Suites (Software); Viterbi algorithm detectors; United States
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-019-3019-7

HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous proteins. We developed a single-instruction multiple-data (SIMD) vectorized implementation of the Viterbi algorithm for profile HMM alignment and introduced various other speed-ups. These accelerated the search methods HHsearch by a factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is \10x faster than PSI-BLAST and \20x faster than HMMER3. Jobs to perform HHsearch and HHblits searches with many query profile HMMs can be parallelized over cores and over cluster servers using OpenMP and message passing interface (MPI). The free, open-source, GPLv3-licensed software is available at https://github.com/soedinglab/hh-suite. The added functionalities and increased speed of HHsearch and HHblits should facilitate their use in large-scale protein structure and function prediction, e.g. in metagenomics and genomics projects.