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It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous proteins.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      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 \u223c10\u00d7 faster than PSI-BLAST and \u223c20\u00d7 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\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/soedinglab\/hh-suite\">https:\/\/github.com\/soedinglab\/hh-suite<\/jats:ext-link>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-019-3019-7","type":"journal-article","created":{"date-parts":[[2019,9,14]],"date-time":"2019-09-14T01:02:37Z","timestamp":1568422957000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1142,"title":["HH-suite3 for fast remote homology detection and deep protein annotation"],"prefix":"10.1186","volume":"20","author":[{"given":"Martin","family":"Steinegger","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"Meier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milot","family":"Mirdita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harald","family":"V\u00f6hringer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephan J.","family":"Haunsberger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9642-8244","authenticated-orcid":false,"given":"Johannes","family":"S\u00f6ding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,9,14]]},"reference":[{"issue":"13","key":"3019_CR1","doi-asserted-by":"publisher","first-page":"4904","DOI":"10.1073\/pnas.1402564111","volume":"111","author":"AC Howe","year":"2014","unstructured":"Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tiedje JM, Brown CT. 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