{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:01:15Z","timestamp":1761742875522},"reference-count":11,"publisher":"World Scientific Pub Co Pte Lt","issue":"06","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Found. Comput. Sci."],"published-print":{"date-parts":[[2006,12]]},"abstract":"<jats:p> Local similarity computation between two sequences permits detecting all the relevant alignments present between subsequences thereof. A well-known dynamic programming algorithm works in time O(mn), m and n being the lengths of the subsequences. The algorithm is rather slow when applied over many sequence pairs. In this paper we present the first bit-parallel computation of the score matrix, for a simplified choice of scores. If the computer word has w bits, then the resulting algorithm works in O(mn log min (m, n, w)\/w) time, achieving up to 8-fold speedups in practice. Some DNA comparison applications use precisely the simplified scores we handle, and thus our algorithm is directly applicable. In others, our method could be used as a raw filter to discard most of the strings, so the classical algorithm can be focused only on the substring pairs that can yield relevant results. <\/jats:p>","DOI":"10.1142\/s0129054106004443","type":"journal-article","created":{"date-parts":[[2006,12,13]],"date-time":"2006-12-13T12:02:04Z","timestamp":1166011324000},"page":"1325-1344","source":"Crossref","is-referenced-by-count":4,"title":["BIT-PARALLEL COMPUTATION OF LOCAL SIMILARITY SCORE MATRICES WITH UNITARY WEIGHTS"],"prefix":"10.1142","volume":"17","author":[{"given":"HEIKKI","family":"HYYR\u00d6","sequence":"first","affiliation":[{"name":"Department of Computer Sciences, University of Tampere, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"GONZALO","family":"NAVARRO","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Chile, Chile"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2011,11,20]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1145\/135239.135243"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1142\/S0129054102000947"},{"key":"rf3","first-page":"89","volume":"56","author":"Crochemore M.","journal-title":"Fundamenta Informaticae"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511574931"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1007\/s00453-004-1108-z"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1016\/0022-0000(80)90002-1"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1145\/316542.316550"},{"key":"rf10","doi-asserted-by":"publisher","DOI":"10.1145\/375360.375365"},{"key":"rf11","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9781316135228"},{"key":"rf12","doi-asserted-by":"publisher","DOI":"10.1504\/IJBRA.2006.009763"},{"key":"rf14","doi-asserted-by":"publisher","DOI":"10.1007\/BF01942606"}],"container-title":["International Journal of Foundations of Computer Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0129054106004443","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T15:27:33Z","timestamp":1565191653000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0129054106004443"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,12]]},"references-count":11,"journal-issue":{"issue":"06","published-online":{"date-parts":[[2011,11,20]]},"published-print":{"date-parts":[[2006,12]]}},"alternative-id":["10.1142\/S0129054106004443"],"URL":"https:\/\/doi.org\/10.1142\/s0129054106004443","relation":{},"ISSN":["0129-0541","1793-6373"],"issn-type":[{"value":"0129-0541","type":"print"},{"value":"1793-6373","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,12]]}}}