{"id":"https://openalex.org/W2078506291","doi":"https://doi.org/10.1145/2460216.2460229","title":"Performance comparison of GPU programming frameworks with the striped Smith-Waterman algorithm","display_name":"Performance comparison of GPU programming frameworks with the striped Smith-Waterman algorithm","publication_year":2012,"publication_date":"2012-03-25","ids":{"openalex":"https://openalex.org/W2078506291","doi":"https://doi.org/10.1145/2460216.2460229","mag":"2078506291"},"language":"en","primary_location":{"id":"doi:10.1145/2460216.2460229","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2460216.2460229","pdf_url":null,"source":{"id":"https://openalex.org/S4210193905","display_name":"ACM SIGARCH Computer Architecture News","issn_l":"0163-5964","issn":["0163-5964","1943-5851"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320740","host_organization_name":"ACM SIGARCH","host_organization_lineage":["https://openalex.org/P4310320740"],"host_organization_lineage_names":["ACM SIGARCH"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM SIGARCH Computer Architecture News","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075512856","display_name":"Takeshi Kakimoto","orcid":null},"institutions":[{"id":"https://openalex.org/I43777268","display_name":"Nagasaki University","ror":"https://ror.org/058h74p94","country_code":"JP","type":"education","lineage":["https://openalex.org/I43777268"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takeshi Kakimoto","raw_affiliation_strings":["Nagasaki University, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nagasaki University, Japan","institution_ids":["https://openalex.org/I43777268"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011267871","display_name":"Keisuke Dohi","orcid":null},"institutions":[{"id":"https://openalex.org/I43777268","display_name":"Nagasaki University","ror":"https://ror.org/058h74p94","country_code":"JP","type":"education","lineage":["https://openalex.org/I43777268"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Keisuke Dohi","raw_affiliation_strings":["Nagasaki University, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nagasaki University, Japan","institution_ids":["https://openalex.org/I43777268"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106183057","display_name":"Yuichiro Shibata","orcid":null},"institutions":[{"id":"https://openalex.org/I43777268","display_name":"Nagasaki University","ror":"https://ror.org/058h74p94","country_code":"JP","type":"education","lineage":["https://openalex.org/I43777268"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuichiro Shibata","raw_affiliation_strings":["Nagasaki University, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nagasaki University, Japan","institution_ids":["https://openalex.org/I43777268"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111880500","display_name":"Kiyoshi Oguri","orcid":null},"institutions":[{"id":"https://openalex.org/I43777268","display_name":"Nagasaki University","ror":"https://ror.org/058h74p94","country_code":"JP","type":"education","lineage":["https://openalex.org/I43777268"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kiyoshi Oguri","raw_affiliation_strings":["Nagasaki University, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nagasaki University, Japan","institution_ids":["https://openalex.org/I43777268"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I43777268"],"apc_list":null,"apc_paid":null,"fwci":0.3973,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.61955551,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"40","issue":"5","first_page":"70","last_page":"75"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.995199978351593,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9837999939918518,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.8828200101852417},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8724250197410583},{"id":"https://openalex.org/keywords/compiler","display_name":"Compiler","score":0.7929996252059937},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7876276969909668},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.6320961117744446},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.6175315380096436},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.5171646475791931},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.43814417719841003},{"id":"https://openalex.org/keywords/programming-paradigm","display_name":"Programming paradigm","score":0.43431276082992554},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4176105558872223},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.34915491938591003},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32105183601379395},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.24453192949295044},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.2088780701160431},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.12666848301887512},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.10230118036270142}],"concepts":[{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.8828200101852417},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8724250197410583},{"id":"https://openalex.org/C169590947","wikidata":"https://www.wikidata.org/wiki/Q47506","display_name":"Compiler","level":2,"score":0.7929996252059937},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7876276969909668},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.6320961117744446},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.6175315380096436},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.5171646475791931},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.43814417719841003},{"id":"https://openalex.org/C34165917","wikidata":"https://www.wikidata.org/wiki/Q188267","display_name":"Programming paradigm","level":2,"score":0.43431276082992554},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4176105558872223},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.34915491938591003},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32105183601379395},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.24453192949295044},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.2088780701160431},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.12666848301887512},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.10230118036270142},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2460216.2460229","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2460216.2460229","pdf_url":null,"source":{"id":"https://openalex.org/S4210193905","display_name":"ACM SIGARCH Computer Architecture News","issn_l":"0163-5964","issn":["0163-5964","1943-5851"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320740","host_organization_name":"ACM SIGARCH","host_organization_lineage":["https://openalex.org/P4310320740"],"host_organization_lineage_names":["ACM SIGARCH"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM SIGARCH Computer Architecture News","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.5400000214576721,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W2011652244","https://openalex.org/W2013733655","https://openalex.org/W2034601083","https://openalex.org/W2068448872","https://openalex.org/W2087064593","https://openalex.org/W2132967231","https://openalex.org/W2133098231","https://openalex.org/W2143210482","https://openalex.org/W2146379626","https://openalex.org/W2154786353","https://openalex.org/W2156140864","https://openalex.org/W2165949232","https://openalex.org/W2184753910"],"related_works":["https://openalex.org/W1963859303","https://openalex.org/W2364044215","https://openalex.org/W2389600408","https://openalex.org/W240129890","https://openalex.org/W3048701459","https://openalex.org/W2149078538","https://openalex.org/W2080146221","https://openalex.org/W2370314112","https://openalex.org/W1912958759","https://openalex.org/W2792081825"],"abstract_inverted_index":{"This":[0],"paper":[1],"evaluates":[2],"and":[3,39,45,54,90,107],"discusses":[4],"how":[5],"different":[6],"GPU":[7,15,31],"programming":[8],"frameworks":[9,48],"affect":[10],"the":[11,18,34,43,46,65,72,76,96,100,103,116,121],"performance":[12],"obtained":[13],"from":[14],"acceleration":[16],"of":[17,29,33,56,105,115],"striped":[19],"smith-waterman":[20],"algorithm":[21,35],"used":[22],"for":[23,59,82,120],"biological":[24],"sequence":[25],"alignment.":[26],"A":[27],"total":[28],"6":[30],"implementations":[32],"on":[36],"NVIDIA":[37],"GT200b":[38],"AMD":[40],"RV870":[41,108],"using":[42],"CUDA":[44,77],"OpenCL":[47,97,106],"are":[49,78,92],"compared":[50],"to":[51],"analyze":[52],"cons":[53],"pros":[55],"explicit":[57],"descriptions":[58,74],"architecture":[60,117],"specific":[61],"hardware":[62],"mechanisms":[63],"in":[64],"code.":[66],"The":[67],"evaluation":[68],"results":[69],"show":[70],"that":[71],"primitive":[73],"with":[75],"still":[79],"efficient":[80,119],"especially":[81],"small":[83],"size":[84],"data,":[85],"while":[86],"better":[87],"instruction":[88],"scheduling":[89],"optimizations":[91],"carried":[93],"out":[94],"by":[95],"compiler.":[98],"On":[99],"other":[101],"hand,":[102],"combination":[104],"which":[109],"provides":[110],"a":[111],"relatively":[112],"simple":[113],"view":[114],"is":[118],"large":[122],"data":[123],"size.":[124]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}