{"id":11245,"date":"2014-01-14T23:39:18","date_gmt":"2014-01-14T21:39:18","guid":{"rendered":"http:\/\/hgpu.org\/?p=11245"},"modified":"2014-01-14T23:39:18","modified_gmt":"2014-01-14T21:39:18","slug":"optimal-alignment-of-three-sequences-on-a-gpu","status":"publish","type":"post","link":"https:\/\/hgpu.org\/?p=11245","title":{"rendered":"Optimal Alignment of Three Sequences On A GPU"},"content":{"rendered":"<p>We develop two algorithms-layered and sloped-to align three sequences on a GPU. Our algorithms can be used to determine the alignment score as well as the actual alignment. Experiments conducted using an NVIDIA C2050 GPU show that our sloped algorithm is 3 times as fast as the layered one. Further, the sloped algorithm delivers a speedup of up to 90 relative to the single core algorithm running on our host CPU when determining the score of the best alignment and a speedup between 21 and 56 when computing the best alignment as well as its score.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>We develop two algorithms-layered and sloped-to align three sequences on a GPU. Our algorithms can be used to determine the alignment score as well as the actual alignment. Experiments conducted using an NVIDIA C2050 GPU show that our sloped algorithm is 3 times as fast as the layered one. Further, the sloped algorithm delivers a [&hellip;]<\/p>\n","protected":false},"author":351,"featured_media":0,"comment_status":"open","ping_status":"closed","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":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[36,10,89,3],"tags":[1787,123,1781,14,20,378],"class_list":["post-11245","post","type-post","status-publish","format-standard","hentry","category-algorithms","category-biology","category-nvidia-cuda","category-paper","tag-algorithms","tag-bioinformatics","tag-biology","tag-cuda","tag-nvidia","tag-tesla-c2050"],"views":2087,"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/11245","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=11245"}],"version-history":[{"count":0,"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/11245\/revisions"}],"wp:attachment":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=11245"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=11245"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=11245"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}