[HTML][HTML] HH-suite3 for fast remote homology detection and deep protein annotation
BMC bioinformatics, 2019•Springer
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 proteins. 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. These accelerated the search methods HHsearch by a factor 4 and …
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. 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. These accelerated the search methods HHsearch by a factor 4 and …
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 proteins.
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. 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 .
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.
Springer