{"id":14763,"date":"2015-10-27T01:21:00","date_gmt":"2015-10-26T23:21:00","guid":{"rendered":"http:\/\/hgpu.org\/?p=14763"},"modified":"2015-10-27T01:21:00","modified_gmt":"2015-10-26T23:21:00","slug":"pairwise-sequence-alignment-with-gaps-with-gpu","status":"publish","type":"post","link":"https:\/\/hgpu.org\/?p=14763","title":{"rendered":"Pairwise Sequence Alignment with Gaps with GPU"},"content":{"rendered":"<p>In this paper we consider the pair-wise sequence alignment problem with gaps, which is motivated by the resequencing problem that requires to assemble short reads sequences into a genome sequence by referring to a reference sequence. The problem has been studied before for single gap and bounded number of gaps. For single gap, there was a GPU-based algorithm proposed. In our work we propose a GPU-based algorithm for the bounded number of gaps case. We implemented the algorithm and compare the performance with the CPU-based algorithm in a multithreadded environment; the results are promising with the GPU version achieving a speedup of 30 times.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>In this paper we consider the pair-wise sequence alignment problem with gaps, which is motivated by the resequencing problem that requires to assemble short reads sequences into a genome sequence by referring to a reference sequence. The problem has been studied before for single gap and bounded number of gaps. For single gap, there was [&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":[36,10,89,90,3],"tags":[1787,123,1781,14,20,1452,1793,209],"class_list":["post-14763","post","type-post","status-publish","format-standard","hentry","category-algorithms","category-biology","category-nvidia-cuda","category-opencl","category-paper","tag-algorithms","tag-bioinformatics","tag-biology","tag-cuda","tag-nvidia","tag-nvidia-geforce-gtx-650","tag-opencl","tag-sequence-alignment"],"views":2193,"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/14763","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=14763"}],"version-history":[{"count":0,"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/14763\/revisions"}],"wp:attachment":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14763"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14763"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14763"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}