Peer Reviewed

1

Document Type

Article

Publication Date

14-9-2019

Keywords

Homology detection, Sequence search, Protein alignment, Algorithm, Profile HMM, SIMD, Functional annotation.

Funder/Sponsor

European Research Council’s Horizon 2020 Framework Programme for Research and Innovation (“Virus-X”, project no. 685778).

Comments

The original article is available at www.biomedcentral.com

Abstract

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.

Disciplines

Physics | Physiology

Citation

Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger SJ, Söding J. HH-suite3 for fast remote homology detection and deep protein annotation. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics. 2019;20(1):473.

PubMed ID

31521110

DOI Link

10.1186/s12859-019-3019-7

Creative Commons License

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.

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