Open Access

BMC Bioinformatics, volume 20, issue 1, publication number 473

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

Hide authors affiliations Show authors affiliations: 4 affiliations

Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Munich, Germany |

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA |

European Bioinformatics Institute, Cambridge, United Kingdom |

⁴

Royal College of Surgeons, Dublin, Ireland |

Publication type: Journal Article

Publication date: 2019-09-14

Springer Nature

Journal: BMC Bioinformatics

Quartile SCImago

Quartile WOS

Impact factor: 3

ISSN: 14712105, 14712105

DOI: 10.1186/s12859-019-3019-7

Copy DOI

PubMed ID: 31521110

Biochemistry

Computer Science Applications

Molecular Biology

Structural Biology

Applied Mathematics

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.

By date By citations

Top-30

Citations by journals

	5 10 15 20 25 30 35
Bioinformatics	Bioinformatics, 32, 4.25% Bioinformatics 32 publications, 4.25%
Nature Communications	Nature Communications, 29, 3.85% Nature Communications 29 publications, 3.85%
Proteins: Structure, Function and Genetics	Proteins: Structure, Function and Genetics, 18, 2.39% Proteins: Structure, Function and Genetics 18 publications, 2.39%
Nucleic Acids Research	Nucleic Acids Research, 18, 2.39% Nucleic Acids Research 18 publications, 2.39%
Viruses	Viruses, 15, 1.99% Viruses 15 publications, 1.99%
Scientific Reports	Scientific Reports, 14, 1.86% Scientific Reports 14 publications, 1.86%
Briefings in Bioinformatics	Briefings in Bioinformatics, 14, 1.86% Briefings in Bioinformatics 14 publications, 1.86%
eLife	eLife, 14, 1.86% eLife 14 publications, 1.86%
Nature Microbiology	Nature Microbiology, 11, 1.46% Nature Microbiology 11 publications, 1.46%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 11, 1.46% International Journal of Molecular Sciences 11 publications, 1.46%
PLoS Computational Biology	PLoS Computational Biology, 10, 1.33% PLoS Computational Biology 10 publications, 1.33%
Nature	Nature, 10, 1.33% Nature 10 publications, 1.33%
Science	Science, 10, 1.33% Science 10 publications, 1.33%
Computational and Structural Biotechnology Journal	Computational and Structural Biotechnology Journal, 10, 1.33% Computational and Structural Biotechnology Journal 10 publications, 1.33%
Proceedings of the National Academy of Sciences of the United States of America	Proceedings of the National Academy of Sciences of the United States of America, 10, 1.33% Proceedings of the National Academy of Sciences of the United States of America 10 publications, 1.33%
Journal of Molecular Biology	Journal of Molecular Biology, 9, 1.2% Journal of Molecular Biology 9 publications, 1.2%
Protein Science	Protein Science, 7, 0.93% Protein Science 7 publications, 0.93%
Frontiers in Microbiology	Frontiers in Microbiology, 7, 0.93% Frontiers in Microbiology 7 publications, 0.93%
Cell Reports	Cell Reports, 7, 0.93% Cell Reports 7 publications, 0.93%
Journal of Chemical Information and Modeling	Journal of Chemical Information and Modeling, 7, 0.93% Journal of Chemical Information and Modeling 7 publications, 0.93%
Methods in Molecular Biology	Methods in Molecular Biology, 7, 0.93% Methods in Molecular Biology 7 publications, 0.93%
Computers in Biology and Medicine	Computers in Biology and Medicine, 6, 0.8% Computers in Biology and Medicine 6 publications, 0.8%
Cell	Cell, 6, 0.8% Cell 6 publications, 0.8%
Molecular Biology and Evolution	Molecular Biology and Evolution, 6, 0.8% Molecular Biology and Evolution 6 publications, 0.8%
Communications Biology	Communications Biology, 5, 0.66% Communications Biology 5 publications, 0.66%
Microbiology spectrum	Microbiology spectrum, 5, 0.66% Microbiology spectrum 5 publications, 0.66%
Acta Crystallographica Section D: Structural Biology	Acta Crystallographica Section D: Structural Biology, 4, 0.53% Acta Crystallographica Section D: Structural Biology 4 publications, 0.53%
BMC Biology	BMC Biology, 4, 0.53% BMC Biology 4 publications, 0.53%
Frontiers in Bioinformatics	Frontiers in Bioinformatics, 4, 0.53% Frontiers in Bioinformatics 4 publications, 0.53%
	5 10 15 20 25 30 35

Citations by publishers

	20 40 60 80 100 120 140 160 180
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 168, 22.31% Cold Spring Harbor Laboratory 168 publications, 22.31%
Springer Nature	Springer Nature, 141, 18.73% Springer Nature 141 publications, 18.73%
Oxford University Press	Oxford University Press, 86, 11.42% Oxford University Press 86 publications, 11.42%
Elsevier	Elsevier, 85, 11.29% Elsevier 85 publications, 11.29%
Wiley	Wiley, 46, 6.11% Wiley 46 publications, 6.11%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 43, 5.71% Multidisciplinary Digital Publishing Institute (MDPI) 43 publications, 5.71%
Frontiers Media S.A.	Frontiers Media S.A., 27, 3.59% Frontiers Media S.A. 27 publications, 3.59%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 17, 2.26% Public Library of Science (PLoS) 17 publications, 2.26%
American Chemical Society (ACS)	American Chemical Society (ACS), 15, 1.99% American Chemical Society (ACS) 15 publications, 1.99%
American Society for Microbiology	American Society for Microbiology, 15, 1.99% American Society for Microbiology 15 publications, 1.99%
eLife Sciences Publications	eLife Sciences Publications, 14, 1.86% eLife Sciences Publications 14 publications, 1.86%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 13, 1.73% American Association for the Advancement of Science (AAAS) 13 publications, 1.73%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 10, 1.33% Proceedings of the National Academy of Sciences (PNAS) 10 publications, 1.33%
International Union of Crystallography (IUCr)	International Union of Crystallography (IUCr), 5, 0.66% International Union of Crystallography (IUCr) 5 publications, 0.66%
Taylor & Francis	Taylor & Francis, 5, 0.66% Taylor & Francis 5 publications, 0.66%
The Company of Biologists	The Company of Biologists, 3, 0.4% The Company of Biologists 3 publications, 0.4%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 3, 0.4% American Society for Biochemistry and Molecular Biology 3 publications, 0.4%
Microbiology Society	Microbiology Society, 2, 0.27% Microbiology Society 2 publications, 0.27%
Portland Press	Portland Press, 2, 0.27% Portland Press 2 publications, 0.27%
King Saud University	King Saud University, 2, 0.27% King Saud University 2 publications, 0.27%
IGI Global	IGI Global, 2, 0.27% IGI Global 2 publications, 0.27%
Research Square Platform LLC	Research Square Platform LLC, 2, 0.27% Research Square Platform LLC 2 publications, 0.27%
American Society for Clinical Investigation	American Society for Clinical Investigation, 1, 0.13% American Society for Clinical Investigation 1 publication, 0.13%
EDP Sciences	EDP Sciences, 1, 0.13% EDP Sciences 1 publication, 0.13%
Impact Journals	Impact Journals, 1, 0.13% Impact Journals 1 publication, 0.13%
The Royal Society	The Royal Society, 1, 0.13% The Royal Society 1 publication, 0.13%
Physical Society of Japan	Physical Society of Japan, 1, 0.13% Physical Society of Japan 1 publication, 0.13%
Gabonatermesztesi Kutato Kozhasznu Tarsasag/Cereal Research Non-Profit Company	Gabonatermesztesi Kutato Kozhasznu Tarsasag/Cereal Research Non-Profit Company, 1, 0.13% Gabonatermesztesi Kutato Kozhasznu Tarsasag/Cereal Research Non-Profit Company 1 publication, 0.13%
Pleiades Publishing	Pleiades Publishing, 1, 0.13% Pleiades Publishing 1 publication, 0.13%
	20 40 60 80 100 120 140 160 180

We do not take into account publications without a DOI.
Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
Statistics recalculated weekly.

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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

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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 00:00:00

PB - Springer Nature

IS - 1

VL - 20

PMID - 31521110

SN - 1471-2105

ER -

BibTex

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BibTex Copy

@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},

doi = {10.1186/s12859-019-3019-7}

}

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Publisher

Springer Nature

Journal

BMC Bioinformatics

Quartile SCImago

Quartile WOS

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ISSN

14712105 (Print)
14712105 (Electronic)