PT  - JOURNAL ARTICLE
AU  - Martin Steinegger
AU  - Markus Meier
AU  - Milot Mirdita
AU  - Harald Vöhringer
AU  - Stephan J. Haunsberger
AU  - Johannes Söding
TI  - HH-suite3 for fast remote homology detection and deep protein annotation
AID  - 10.1101/560029
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 560029
4099  - http://biorxiv.org/content/early/2019/02/25/560029.short
4100  - http://biorxiv.org/content/early/2019/02/25/560029.full
AB  - Background 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 sequences.Results We developed a single-instruction multiple-data (SIMD) vectorized implementation of the Viterbi algorithm for profile HMM alignment and introduced various other speed-ups. This accelerated 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 servers in a cluster using OpenMP and message passing interface (MPI). The free, open-source, GNU GPL(v3)-licensed software is available at https://github.com/soedinglab/hh-suite.Conclusion 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.MSA:multiple sequence alignment;HMM:hidden Markov model;SIMD:single-instruction multiple-data;SSSE3:supplemental streaming SIMD extensions 3;AVX2:advanced vector extension (SIMD instruction set standards);