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

View ORCID ProfileMartin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, View ORCID ProfileJohannes Söding
doi: https://doi.org/10.1101/560029
Martin Steinegger
1Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
2Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
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  • ORCID record for Martin Steinegger
Markus Meier
1Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Milot Mirdita
1Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Harald Vöhringer
1Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
4European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom
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Stephan J. Haunsberger
5Royal College of Surgeons, Dublin D02 YN77, Ireland
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Johannes Söding
1Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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  • For correspondence: soeding@mpibpc.mpg.de
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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 sequences.

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. This accelerated 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 servers in a cluster using OpenMP and message passing interface (MPI). The free, open-source, GNU GPL(v3)-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.

  • Abbreviations

    MSA
    :multiple sequence alignment;
    HMM
    :hidden Markov model;
    SIMD
    :single-instruction multiple-data;
    SSSE3
    :supplemental streaming SIMD extensions 3;
    AVX2
    :advanced vector extension (SIMD instruction set standards);
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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    HH-suite3 for fast remote homology detection and deep protein annotation
    Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding
    bioRxiv 560029; doi: https://doi.org/10.1101/560029
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    HH-suite3 for fast remote homology detection and deep protein annotation
    Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding
    bioRxiv 560029; doi: https://doi.org/10.1101/560029

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