ArticleBMC bioinformatics2019
HH-suite3 for fast remote homology detection and deep protein annotation.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 619 papers.
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619 citing papers in PubMed.
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- Hawaiian geothermal fumaroles contain diverse and novel viruses.Microbiology spectrum · 2026Article
- Stoic: fast and accurate protein stoichiometry prediction.Bioinformatics (Oxford, England) · 2026Article
- Computer-Aided Identification and Molecular Interaction Analyses of Annona muricata Acetogenins Against LuxS.Biotechnology and applied biochemistry · 2026Article
- WASP: a pipeline for functional annotation prediction based on AlphaFold structural models.Nature communications · 2026Article
- SEVA: structural and evolutionary feature integration for predicting virulence factors and antibiotic resistance genes.Microbiome · 2026Article
- TEDLH: domain HMMs for sensitive detection of remote homologues.Bioinformatics (Oxford, England) · 2026Article
- Evolutionarily conserved short linear motifs drive actin filament binding.Nature cell biology · 2026Article
559 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
backgroundHH-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.
resultsWe 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 ∼10× faster than PSI-BLAST and ∼20× 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 .
conclusionThe 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.
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