{"id":"https://openalex.org/W2057795393","doi":"https://doi.org/10.1109/bibe.2008.4696721","title":"Design and implementation of the Smith-Waterman algorithm on the CUDA-compatible GPU","display_name":"Design and implementation of the Smith-Waterman algorithm on the CUDA-compatible GPU","publication_year":2008,"publication_date":"2008-10-01","ids":{"openalex":"https://openalex.org/W2057795393","doi":"https://doi.org/10.1109/bibe.2008.4696721","mag":"2057795393"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2008.4696721","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2008.4696721","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 8th IEEE International Conference on BioInformatics and BioEngineering","raw_type":"proceedings-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/A5083643010","display_name":"Yuma Munekawa","orcid":null},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"Osaka University","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yuma Munekawa","raw_affiliation_strings":["Graduate School of Information Science and Technology, Osaka University, Osaka, Japan","Grad. Sch. of Inf. Sci. & Technol., Osaka Univ., Toyonaka"],"affiliations":[{"raw_affiliation_string":"Graduate School of Information Science and Technology, Osaka University, Osaka, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Grad. Sch. of Inf. Sci. & Technol., Osaka Univ., Toyonaka","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090008684","display_name":"Fumihiko Ino","orcid":"https://orcid.org/0000-0002-5757-7631"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"Osaka University","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Fumihiko Ino","raw_affiliation_strings":["Graduate School of Information Science and Technology, Osaka University, Osaka, Japan","Grad. Sch. of Inf. Sci. & Technol., Osaka Univ., Toyonaka"],"affiliations":[{"raw_affiliation_string":"Graduate School of Information Science and Technology, Osaka University, Osaka, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Grad. Sch. of Inf. Sci. & Technol., Osaka Univ., Toyonaka","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111729293","display_name":"Kenichi Hagihara","orcid":null},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"Osaka University","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kenichi Hagihara","raw_affiliation_strings":["Graduate School of Information Science and Technology, Osaka University, Osaka, Japan","Grad. Sch. of Inf. Sci. & Technol., Osaka Univ., Toyonaka"],"affiliations":[{"raw_affiliation_string":"Graduate School of Information Science and Technology, Osaka University, Osaka, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Grad. Sch. of Inf. Sci. & Technol., Osaka Univ., Toyonaka","institution_ids":["https://openalex.org/I98285908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5083643010"],"corresponding_institution_ids":["https://openalex.org/I98285908"],"apc_list":null,"apc_paid":null,"fwci":10.0379,"has_fulltext":false,"cited_by_count":45,"citation_normalized_percentile":{"value":0.97880957,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.991599977016449,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.991599977016449,"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/T10839","display_name":"Pancreatic function and diabetes","score":0.9890000224113464,"subfield":{"id":"https://openalex.org/subfields/2746","display_name":"Surgery"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11321","display_name":"Error Correcting Code Techniques","score":0.9868999719619751,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.9074885845184326},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.859572172164917},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7801331281661987},{"id":"https://openalex.org/keywords/opengl","display_name":"OpenGL","score":0.7784607410430908},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7724515199661255},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.7152525186538696},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.581510603427887},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.5107641220092773},{"id":"https://openalex.org/keywords/coprocessor","display_name":"Coprocessor","score":0.44250285625457764},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.4315708577632904},{"id":"https://openalex.org/keywords/shared-memory","display_name":"Shared memory","score":0.4282245337963104},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34731289744377136},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.1852857768535614},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.10102349519729614},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.09513157606124878},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.08245781064033508}],"concepts":[{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.9074885845184326},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.859572172164917},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7801331281661987},{"id":"https://openalex.org/C2778305236","wikidata":"https://www.wikidata.org/wiki/Q178570","display_name":"OpenGL","level":3,"score":0.7784607410430908},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7724515199661255},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.7152525186538696},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.581510603427887},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.5107641220092773},{"id":"https://openalex.org/C86111242","wikidata":"https://www.wikidata.org/wiki/Q859595","display_name":"Coprocessor","level":2,"score":0.44250285625457764},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.4315708577632904},{"id":"https://openalex.org/C133875982","wikidata":"https://www.wikidata.org/wiki/Q764810","display_name":"Shared memory","level":2,"score":0.4282245337963104},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34731289744377136},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.1852857768535614},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.10102349519729614},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.09513157606124878},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.08245781064033508},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe.2008.4696721","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2008.4696721","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 8th IEEE International Conference on BioInformatics and BioEngineering","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.49000000953674316}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1992519395","https://openalex.org/W2003144438","https://openalex.org/W2006899413","https://openalex.org/W2011652244","https://openalex.org/W2055043387","https://openalex.org/W2061833373","https://openalex.org/W2087064593","https://openalex.org/W2089499735","https://openalex.org/W2116508956","https://openalex.org/W2146379626","https://openalex.org/W2166621589","https://openalex.org/W2169706611","https://openalex.org/W2295862081","https://openalex.org/W2988817687","https://openalex.org/W4236236547","https://openalex.org/W4241667468","https://openalex.org/W4247964656","https://openalex.org/W4250981202"],"related_works":["https://openalex.org/W2137567370","https://openalex.org/W2347732685","https://openalex.org/W2364238223","https://openalex.org/W1991259050","https://openalex.org/W2565862224","https://openalex.org/W2342866599","https://openalex.org/W2147073383","https://openalex.org/W2154903817","https://openalex.org/W167388389","https://openalex.org/W2165949232"],"abstract_inverted_index":{"This":[0,135],"paper":[1],"describes":[2],"a":[3,68,91,100,124,143],"design":[4],"and":[5,52,74],"implementation":[6],"of":[7,63,102,118,127],"the":[8,13,32,44,56,61,83,93,96,116],"Smith-Waterman":[9],"algorithm":[10],"accelerated":[11],"on":[12,31],"graphics":[14],"processing":[15,53],"unit":[16],"(GPU).":[17],"Our":[18],"method":[19,36,85,98],"is":[20,29,137],"implemented":[21],"using":[22,105],"compute":[23],"unified":[24],"device":[25],"architecture":[26],"(CUDA),":[27],"which":[28],"available":[30],"nVIDIA":[33],"GPU.":[34,57],"The":[35],"efficiently":[37],"uses":[38],"on-chip":[39],"shared":[40,113],"memory":[41,51,114],"to":[42,72,121],"reduce":[43],"data":[45,64,69,119],"amount":[46,117],"being":[47],"transferred":[48],"between":[49],"off-chip":[50],"elements":[54],"in":[55],"Furthermore,":[58],"it":[59],"reduces":[60,115],"number":[62],"fetches":[65,120],"by":[66],"applying":[67],"reuse":[70],"technique":[71],"query":[73],"database":[75],"sequences.":[76],"We":[77],"show":[78],"some":[79],"experimental":[80],"results":[81],"comparing":[82],"proposed":[84],"with":[86],"an":[87],"OpenGL-based":[88,97],"method.":[89],"As":[90],"result,":[92],"speedup":[94],"over":[95],"reaches":[99],"factor":[101],"6.4":[103],"when":[104],"amino":[106],"acid":[107],"sequence":[108],"database.We":[109],"also":[110],"find":[111],"that":[112],"1/140,":[122],"providing":[123],"peak":[125],"performance":[126,136],"5.65":[128],"giga":[129],"cell":[130],"updates":[131],"per":[132],"second":[133],"(GCUPS).":[134],"approximately":[138],"three":[139],"times":[140],"faster":[141],"than":[142],"prior":[144],"CUDA-based":[145],"implementation.":[146]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":7}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
