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This algorithm achieved 2\u20138 times performance improvement over other SIMD based Smith\u2013Waterman implementations. On a 2.0 GHz Xeon Core 2 Duo processor, speeds of &amp;gt;3.0 billion cell updates\/s were achieved.<\/jats:p><jats:p>Availability: \u00a0<\/jats:p><jats:p>Contact: \u00a0farrar.michael@gmail.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl582","type":"journal-article","created":{"date-parts":[[2006,11,17]],"date-time":"2006-11-17T01:17:37Z","timestamp":1163726257000},"page":"156-161","source":"Crossref","is-referenced-by-count":350,"title":["Striped Smith\u2013Waterman speeds database searches six times over other SIMD implementations"],"prefix":"10.1093","volume":"23","author":[{"given":"Michael","family":"Farrar","sequence":"first","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2006,11,16]]},"reference":[{"key":"2023041107044159100_","doi-asserted-by":"crossref","DOI":"10.1145\/224170.224222","article-title":"Microparallelism and high performance protein matching","author":"Alpern","year":"1995"},{"key":"2023041107044159100_","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023041107044159100_","first-page":"9","article-title":"Realigner: a program for refining DNA sequence multi-alignments","author":"Anson","year":"1997"},{"key":"2023041107044159100_","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/nar\/28.1.15","article-title":"Genbank","volume":"28","author":"Benson","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023041107044159100_","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1089\/cmb.1994.1.271","article-title":"Recent developments in linear-space alignment methods: a survey","volume":"4","author":"Chao","year":"1994","journal-title":"J. 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