Gene

Operating system

Artificial intelligence

Archaeology

Peptide sequence

Parallel computing

Pairwise comparison

Threading (protein sequence)

Hidden Markov model

Annotation

Software

Software suite

Computer science

Sequence alignment

Protein structure

Biochemistry

Viterbi algorithm

Smith–Waterman algorithm

Suite

Biology

Multiple sequence alignment

History

BMC Bioinformatics

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.

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