{"id":4602,"date":"2011-07-06T12:21:16","date_gmt":"2011-07-06T12:21:16","guid":{"rendered":"http:\/\/hgpu.org\/?p=4602"},"modified":"2011-07-06T12:21:16","modified_gmt":"2011-07-06T12:21:16","slug":"striped-smith-waterman-speeds-database-searches-six-times-over-other-simd-implementations","status":"publish","type":"post","link":"https:\/\/hgpu.org\/?p=4602","title":{"rendered":"Striped Smith-Waterman speeds database searches six times over other SIMD implementations"},"content":{"rendered":"<p>MOTIVATION: The only algorithm guaranteed to find the optimal local alignment is the Smith-Waterman. It is also one of the slowest due to the number of computations required for the search. To speed up the algorithm, Single-Instruction Multiple-Data (SIMD) instructions have been used to parallelize the algorithm at the instruction level. RESULTS: A faster implementation of the Smith-Waterman algorithm is presented. This algorithm achieved 2-8 times performance improvement over other SIMD based Smith-Waterman implementations. On a 2.0 GHz Xeon Core 2 Duo processor, speeds of &gt;3.0 billion cell updates\/s were achieved. AVAILABILITY: http:\/\/farrar.michael.googlepages.com\/Smith-waterman<\/p>\n","protected":false},"excerpt":{"rendered":"<p>MOTIVATION: The only algorithm guaranteed to find the optimal local alignment is the Smith-Waterman. It is also one of the slowest due to the number of computations required for the search. To speed up the algorithm, Single-Instruction Multiple-Data (SIMD) instructions have been used to parallelize the algorithm at the instruction level. RESULTS: A faster implementation [&hellip;]<\/p>\n","protected":false},"author":351,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[36,10,3],"tags":[1787,123,1781,209,284],"class_list":["post-4602","post","type-post","status-publish","format-standard","hentry","category-algorithms","category-biology","category-paper","tag-algorithms","tag-bioinformatics","tag-biology","tag-sequence-alignment","tag-smith-waterman-algorithm"],"views":2066,"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/4602","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/users\/351"}],"replies":[{"embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=4602"}],"version-history":[{"count":0,"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/4602\/revisions"}],"wp:attachment":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=4602"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=4602"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=4602"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}