{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:20:13Z","timestamp":1674710413831},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Multiple sequence alignment is an important tool in bioinformatics. Although efficient heuristic algorithms exist for this problem, the exponential growth of biological data demands an even higher throughput. The recent emergence of multi-core technologies has made it possible to achieve a highly improved execution time for many bioinformatics applications. In this article, we introduce an implementation that accelerates the distance matrix computation on x86 and Cell Broadband Engine, a homogeneous and heterogeneous multi-core system, respectively. By taking advantage of multiple processors as well as Single Instruction Multiple Data vectorization, we were able to achieve speed-ups of two orders of magnitude compared to the publicly available implementation utilized in ClustalW.<\/jats:p>\n               <jats:p>Availability and Implementation: Source codes in C are publicly available at https:\/\/sourceforge.net\/projects\/distmatcomp\/<\/jats:p>\n               <jats:p>Contact: \u00a0adri0004@ntu.edu.sg<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq135","type":"journal-article","created":{"date-parts":[[2010,3,28]],"date-time":"2010-03-28T00:14:17Z","timestamp":1269735257000},"page":"1368-1369","source":"Crossref","is-referenced-by-count":6,"title":["Multi-threaded vectorized distance matrix computation on the CELL\/BE and x86\/SSE2 architectures"],"prefix":"10.1093","volume":"26","author":[{"given":"Adrianto","family":"Wirawan","sequence":"first","affiliation":[{"name":"School of Computer Engineering, Nanyang Technological University, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chee Keong","family":"Kwoh","sequence":"additional","affiliation":[{"name":"School of Computer Engineering, Nanyang Technological University, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bertil","family":"Schmidt","sequence":"additional","affiliation":[{"name":"School of Computer Engineering, Nanyang Technological University, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,3,26]]},"reference":[{"key":"2023012507513070500_B1","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1145\/952532.952559","article-title":"A component-based implementation of multiple sequence alignment","volume-title":"Proceedings of the 2003 ACM Symposium on Applied Computing","author":"Catalyurek","year":"2003"},{"key":"2023012507513070500_B2","article-title":"MT-ClustalW: multithreading multiple sequence alignment","author":"Chaichoompu","year":"2006","journal-title":"In the 20th International Parallel and Distributed Processing Symposium, IPDPS 2006."},{"key":"2023012507513070500_B3","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012507513070500_B4","article-title":"Software Development Kit 2.1 Accelerated Library Framework Programmer's Guide and API Reference, Version 1.1","author":"IBM","year":"2007","journal-title":"IBM developerWorks."},{"key":"2023012507513070500_B5","doi-asserted-by":"crossref","first-page":"1585","DOI":"10.1093\/bioinformatics\/btg192","article-title":"ClustalW-MPI: ClustalW analysis using distributed and parallel computing","volume":"19","author":"Li","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012507513070500_B6","doi-asserted-by":"crossref","first-page":"4412","DOI":"10.1073\/pnas.86.12.4412","article-title":"A tool for multiple sequence alignment","volume":"86","author":"Lipman","year":"1989","journal-title":"Proc. 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Notes"},{"key":"2023012507513070500_B13","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"2023012507513070500_B14","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1186\/1471-2105-9-377","article-title":"CBESW: sequence alignment on the playstation 3","volume":"9","author":"Wirawan","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012507513070500_B15","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1007\/978-3-642-01970-8_96","article-title":"Pairwise distance matrix computation for multiple sequence alignment on the cell broadband engine","volume":"5544","author":"Wirawan","year":"2009","journal-title":"Lect. Notes Comput. 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