HH-suite3 for fast remote homology detection and deep protein annotation
HH-suite3 for fast remote homology detection and deep protein annotation
Martin Steinegger,Markus Meier,3 Authors,J. Soeding
TLDR
A single-instruction multiple-data (SIMD) vectorized implementation of the Viterbi algorithm for profile HMM alignment was developed and various other speed-ups were introduced to accelerated the search methods HHsearch and HHblits and should facilitate their use in large-scale protein structure and function prediction, e.g. in metagenomics and genomics projects.
Abstract
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 ∼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. 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.