{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T19:45:07Z","timestamp":1784231107742,"version":"3.55.0"},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2004,12,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Comparison of nucleic acid and protein sequences is a fundamental tool of modern bioinformatics. A dominant method of such string matching is the \u2018seed-and-extend\u2019 approach, in which occurrences of short subsequences called \u2018seeds\u2019 are used to search for potentially longer matches in a large database of sequences. Each such potential match is then checked to see if it extends beyond the seed. To be effective, the seed-and-extend approach needs to catalogue seeds from virtually every substring in the database of search strings. Projects such as mammalian genome assemblies and large-scale protein matching, however, have such large sequence databases that the resulting list of seeds cannot be stored in RAM on a single computer. This significantly slows the matching process.<\/jats:p>\n               <jats:p>Results: We present a simple and elegant method in which only a small fraction of seeds, called \u2018minimizers\u2019, needs to be stored. Using minimizers can speed up string-matching computations by a large factor while missing only a small fraction of the matches found using all seeds.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bth408","type":"journal-article","created":{"date-parts":[[2004,7,16]],"date-time":"2004-07-16T00:17:10Z","timestamp":1089937030000},"page":"3363-3369","source":"Crossref","is-referenced-by-count":462,"title":["Reducing storage requirements for biological sequence comparison"],"prefix":"10.1093","volume":"20","author":[{"given":"Michael","family":"Roberts","sequence":"first","affiliation":[{"name":"Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742-2431, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wayne","family":"Hayes","sequence":"additional","affiliation":[{"name":"Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742-2431, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian R.","family":"Hunt","sequence":"additional","affiliation":[{"name":"Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742-2431, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen M.","family":"Mount","sequence":"additional","affiliation":[{"name":"Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742-2431, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James A.","family":"Yorke","sequence":"additional","affiliation":[{"name":"Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742-2431, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2004,7,15]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/18\/3363\/48906547\/bioinformatics_20_18_3363.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/18\/3363\/48906547\/bioinformatics_20_18_3363.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T16:48:22Z","timestamp":1674665302000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/20\/18\/3363\/202143"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,7,15]]},"references-count":0,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2004,12,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bth408","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2004,12,12]]},"published":{"date-parts":[[2004,7,15]]}}}