HH-suite3 for fast remote homology detection and deep protein annotation
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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-09-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-019-3019-7 |
| _version_ | 1818299378730795008 |
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| author | Martin Steinegger Markus Meier Milot Mirdita Harald Vöhringer Stephan J. Haunsberger Johannes Söding |
| author_facet | Martin Steinegger Markus Meier Milot Mirdita Harald Vöhringer Stephan J. Haunsberger Johannes Söding |
| author_sort | Martin Steinegger |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T04:50:17Z |
| format | Article |
| id | doaj.art-59e6cde7518149c596f2e8cd8b7e6c97 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-13T04:50:17Z |
| publishDate | 2019-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-59e6cde7518149c596f2e8cd8b7e6c972022-12-21T23:59:02ZengBMCBMC Bioinformatics1471-21052019-09-0120111510.1186/s12859-019-3019-7HH-suite3 for fast remote homology detection and deep protein annotationMartin Steinegger0Markus Meier1Milot Mirdita2Harald Vöhringer3Stephan J. Haunsberger4Johannes Söding5Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical ChemistryQuantitative and Computational Biology Group, Max-Planck Institute for Biophysical ChemistryQuantitative and Computational Biology Group, Max-Planck Institute for Biophysical ChemistryQuantitative and Computational Biology Group, Max-Planck Institute for Biophysical ChemistryRoyal College of SurgeonsQuantitative and Computational Biology Group, Max-Planck Institute for Biophysical ChemistryAbstract 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.http://link.springer.com/article/10.1186/s12859-019-3019-7Homology detectionSequence searchProtein alignmentAlgorithmProfile HMMSIMD |
| spellingShingle | Martin Steinegger Markus Meier Milot Mirdita Harald Vöhringer Stephan J. Haunsberger Johannes Söding HH-suite3 for fast remote homology detection and deep protein annotation BMC Bioinformatics Homology detection Sequence search Protein alignment Algorithm Profile HMM SIMD |
| title | HH-suite3 for fast remote homology detection and deep protein annotation |
| title_full | HH-suite3 for fast remote homology detection and deep protein annotation |
| title_fullStr | HH-suite3 for fast remote homology detection and deep protein annotation |
| title_full_unstemmed | HH-suite3 for fast remote homology detection and deep protein annotation |
| title_short | HH-suite3 for fast remote homology detection and deep protein annotation |
| title_sort | hh suite3 for fast remote homology detection and deep protein annotation |
| topic | Homology detection Sequence search Protein alignment Algorithm Profile HMM SIMD |
| url | http://link.springer.com/article/10.1186/s12859-019-3019-7 |
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