{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T19:31:25Z","timestamp":1768591885817,"version":"3.49.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1296,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The PROSITE resource provides a rich and well annotated source of signatures in the form of generalized profiles that allow protein domain detection and functional annotation. One of the major limiting factors in the application of PROSITE in genome and metagenome annotation pipelines is the time required to search protein sequence databases for putative matches. We describe an improved and optimized implementation of the PROSITE search tool pfsearch that, combined with a newly developed heuristic, addresses this limitation. On a modern x86_64 hyper-threaded quad-core desktop computer, the new pfsearchV3 is two orders of magnitude faster than the original algorithm.<\/jats:p>\n               <jats:p>Availability and implementation: Source code and binaries of pfsearchV3 are freely available for download at http:\/\/web.expasy.org\/pftools\/#pfsearchV3, implemented in C and supported on Linux. PROSITE generalized profiles including the heuristic cut-off scores are available at the same address.<\/jats:p>\n               <jats:p>Contact: \u00a0pftools@isb-sib.ch<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt129","type":"journal-article","created":{"date-parts":[[2013,3,17]],"date-time":"2013-03-17T00:54:39Z","timestamp":1363481679000},"page":"1215-1217","source":"Crossref","is-referenced-by-count":27,"title":["pfsearchV3: a code acceleration and heuristic to search PROSITE profiles"],"prefix":"10.1093","volume":"29","author":[{"given":"Thierry","family":"Schuepbach","sequence":"first","affiliation":[{"name":"1 Vital-IT Group, SIB Swiss Institute of Bioinformatics, Genopode, UNIL-Sorge, 1015 Lausanne and 2Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Pagni","sequence":"additional","affiliation":[{"name":"1 Vital-IT Group, SIB Swiss Institute of Bioinformatics, Genopode, UNIL-Sorge, 1015 Lausanne and 2Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alan","family":"Bridge","sequence":"additional","affiliation":[{"name":"1 Vital-IT Group, SIB Swiss Institute of Bioinformatics, Genopode, UNIL-Sorge, 1015 Lausanne and 2Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lydie","family":"Bougueleret","sequence":"additional","affiliation":[{"name":"1 Vital-IT Group, SIB Swiss Institute of Bioinformatics, Genopode, UNIL-Sorge, 1015 Lausanne and 2Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ioannis","family":"Xenarios","sequence":"additional","affiliation":[{"name":"1 Vital-IT Group, SIB Swiss Institute of Bioinformatics, Genopode, UNIL-Sorge, 1015 Lausanne and 2Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland"},{"name":"1 Vital-IT Group, SIB Swiss Institute of Bioinformatics, Genopode, UNIL-Sorge, 1015 Lausanne and 2Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lorenzo","family":"Cerutti","sequence":"additional","affiliation":[{"name":"1 Vital-IT Group, SIB Swiss Institute of Bioinformatics, Genopode, UNIL-Sorge, 1015 Lausanne and 2Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,3,16]]},"reference":[{"key":"2023012810390866300_btt129-B1","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput. Biol."},{"key":"2023012810390866300_btt129-B2","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1038\/nrmicro2832","article-title":"Microbial interactions: from networks to models","volume":"10","author":"Faust","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"2023012810390866300_btt129-B3","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/nature10530","article-title":"A high-resolution map of human evolutionary constraint using 29 mammals","volume":"478","author":"Lindblad-Toh","year":"2011","journal-title":"Nature"},{"key":"2023012810390866300_btt129-B4","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1006\/jmbi.1998.2221","article-title":"Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods","volume":"284","author":"Park","year":"1998","journal-title":"J. Mol. Biol."},{"key":"2023012810390866300_btt129-B5","doi-asserted-by":"crossref","first-page":"D584","DOI":"10.1093\/nar\/gks1157","article-title":"HAMAP in 2013, new developments in the protein family classification and annotation system","volume":"41","author":"Pedruzzi","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012810390866300_btt129-B6","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1093\/bib\/3.3.265","article-title":"PROSITE: a documented database using patterns and profiles as motif descriptors","volume":"3","author":"Sigrist","year":"2002","journal-title":"Brief Bioinform."},{"key":"2023012810390866300_btt129-B7","doi-asserted-by":"crossref","first-page":"D344","DOI":"10.1093\/nar\/gks1067","article-title":"New and continuing developments at PROSITE","volume":"41","author":"Sigrist","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012810390866300_btt129-B8","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1093\/bib\/bbs039","article-title":"Current opportunities and challenges in microbial metagenome analysis\u2013a bioinformatic perspective","volume":"13","author":"Teeling","year":"2012","journal-title":"Brief Bioinform."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/9\/1215\/48901020\/bioinformatics_29_9_1215.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/9\/1215\/48901020\/bioinformatics_29_9_1215.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T12:23:08Z","timestamp":1674908588000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/9\/1215\/223031"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,3,16]]},"references-count":8,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2013,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt129","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,5,1]]},"published":{"date-parts":[[2013,3,16]]}}}