{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T14:24:31Z","timestamp":1777645471667,"version":"3.51.4"},"reference-count":0,"publisher":"SAGE Publications","issue":"1-2","license":[{"start":{"date-parts":[[2009,10,1]],"date-time":"2009-10-01T00:00:00Z","timestamp":1254355200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Fundamenta Informaticae"],"published-print":{"date-parts":[[2009,10]]},"abstract":"<jats:p>Algorithms for estimating similarity between two macromolecular sequences are of profound importance for molecular biology. The standard methods utilize so-called primary structure, that is a string of characters denoting the sequence of monomers in hetero-polymer. These methods find the substrings of maximal similarity, as defined by the so-called similarity matrix, for a pair of two molecules. The problem is solved either by the exact dynamic programming method, or by approximate heuristic methods.<\/jats:p>\n                  <jats:p>The approximate algorithms are almost two orders of magnitude faster in comparison with the standard version of the exact Smith-Waterman algorithm, when executed on the same hardware, hence the exact algorithm is relatively rarely used. Recently a very efficient implementation of Smith- Waterman algorithm utilizing SIMD extensions to the standard instruction set reduced the speed advantage of heuristic algorithms to factor of three. Here we present an improved implementation of the Smith-Waterman algorithm on the Cell processor.<\/jats:p>\n                  <jats:p>Implementation presented here achieves execution speed of approximately 9 GCUPS. The performance is independent on the scoring system. It is 4 to 10 times faster than best Smith-Waterman implementation running on a PC and 1.5 to 3 times faster than the same implementation running on Sony PlayStation 3. It is also 5 times faster than the recent implementation of the Smith- Waterman utilizing Nvidia GPU.<\/jats:p>\n                  <jats:p>Our implementation running on Sony PlayStation 3 has performance which is directly comparable with that of BLAST running on PC, being up to 4 times faster in the best case and no more than two times slower in the worst case. This performance level opens possibility for using the exact Smith-Waterman algorithm in applications, where currently approximate algorithms are used.<\/jats:p>","DOI":"10.3233\/fi-2009-173","type":"journal-article","created":{"date-parts":[[2019,12,2]],"date-time":"2019-12-02T22:59:40Z","timestamp":1575327580000},"page":"181-194","source":"Crossref","is-referenced-by-count":9,"title":["The new SIMD Implementation of the Smith-Waterman Algorithm on \t\t\t Cell Microprocessor"],"prefix":"10.1177","volume":"96","author":[{"given":"Witold R.","family":"Rudnicki","sequence":"first","affiliation":[{"name":"Interdisciplinary Centre for Mathematical and\r\t\t\t Computational Modelling University of Warsaw, Pawi\u0144skiego 5A,\r\t\t\t 02-106 Warszawa, Poland. E-mail: W.Rudnicki@icm.edu.pl"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aleksander","family":"Jankowski","sequence":"additional","affiliation":[{"name":"ajank@students.mimuw.edu.pl"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aleksander","family":"Modzelewski","sequence":"additional","affiliation":[{"name":"aleander@shirk.pl"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aleksander","family":"Piotrowski","sequence":"additional","affiliation":[{"name":"ap219542@students.mimuw.edu.pl"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam","family":"Zadro\u017cny","sequence":"additional","affiliation":[{"name":"Adam.Zadrozny@gmail.com"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"179","published-online":{"date-parts":[[2009,10,1]]},"container-title":["Fundamenta Informaticae"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.3233\/FI-2009-173","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.3233\/FI-2009-173","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T06:32:17Z","timestamp":1777444337000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.3233\/FI-2009-173"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,10]]},"references-count":0,"journal-issue":{"issue":"1-2","published-print":{"date-parts":[[2009,10]]}},"alternative-id":["10.3233\/FI-2009-173"],"URL":"https:\/\/doi.org\/10.3233\/fi-2009-173","relation":{"is-cited-by":[{"id-type":"doi","id":"10.1155\/2013\/721738","asserted-by":"object"}]},"ISSN":["0169-2968","1875-8681"],"issn-type":[{"value":"0169-2968","type":"print"},{"value":"1875-8681","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,10]]}}}