Open Access
HH-suite3 for fast remote homology detection and deep protein annotation
Martin Steinegger
1, 2
,
Markus Meier
1
,
Milot Mirdita
1
,
Harald Vöhringer
1, 3
,
Stephan J Haunsberger
4
,
Johannes Söding
1
4
Royal College of Surgeons, Dublin, Ireland
|
Тип публикации: Journal Article
Дата публикации: 2019-09-14
scimago Q1
wos Q1
БС1
SJR: 1.190
CiteScore: 6.8
Impact factor: 3.3
ISSN: 14712105
PubMed ID:
31521110
Biochemistry
Computer Science Applications
Molecular Biology
Structural Biology
Applied Mathematics
Краткое описание
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
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.
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Steinegger M. et al. HH-suite3 for fast remote homology detection and deep protein annotation // BMC Bioinformatics. 2019. Vol. 20. No. 1. 473
ГОСТ со всеми авторами (до 50)
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Steinegger M., Meier M., Mirdita M., Vöhringer H., Haunsberger S. J., Söding J. HH-suite3 for fast remote homology detection and deep protein annotation // BMC Bioinformatics. 2019. Vol. 20. No. 1. 473
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TY - JOUR
DO - 10.1186/s12859-019-3019-7
UR - https://doi.org/10.1186/s12859-019-3019-7
TI - HH-suite3 for fast remote homology detection and deep protein annotation
T2 - BMC Bioinformatics
AU - Steinegger, Martin
AU - Meier, Markus
AU - Mirdita, Milot
AU - Vöhringer, Harald
AU - Haunsberger, Stephan J
AU - Söding, Johannes
PY - 2019
DA - 2019/09/14
PB - Springer Nature
IS - 1
VL - 20
PMID - 31521110
SN - 1471-2105
ER -
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@article{2019_Steinegger,
author = {Martin Steinegger and Markus Meier and Milot Mirdita and Harald Vöhringer and Stephan J Haunsberger and Johannes Söding},
title = {HH-suite3 for fast remote homology detection and deep protein annotation},
journal = {BMC Bioinformatics},
year = {2019},
volume = {20},
publisher = {Springer Nature},
month = {sep},
url = {https://doi.org/10.1186/s12859-019-3019-7},
number = {1},
pages = {473},
doi = {10.1186/s12859-019-3019-7}
}