{"id":"https://openalex.org/W2109268917","doi":"https://doi.org/10.1186/1471-2105-10-s7-a3","title":"Parallelized pairwise sequence alignment using CUDA on multiple GPUs","display_name":"Parallelized pairwise sequence alignment using CUDA on multiple GPUs","publication_year":2009,"publication_date":"2009-06-01","ids":{"openalex":"https://openalex.org/W2109268917","doi":"https://doi.org/10.1186/1471-2105-10-s7-a3","mag":"2109268917","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3313266"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-s7-a3","doi":"https://doi.org/10.1186/1471-2105-10-s7-a3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s7-a3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S7-A3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S7-A3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030227990","display_name":"Sungbo Jung","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I142740786","display_name":"University of Louisville","ror":"https://ror.org/01ckdn478","country_code":"US","type":"education","lineage":["https://openalex.org/I142740786"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sungbo Jung","raw_affiliation_strings":["Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, 40292, USA","Department of Computer Engineering and Computer Science, University of Louisville, Louisville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, 40292, USA","institution_ids":["https://openalex.org/I142740786"]},{"raw_affiliation_string":"Department of Computer Engineering and Computer Science, University of Louisville, Louisville, USA","institution_ids":["https://openalex.org/I142740786"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5030227990"],"corresponding_institution_ids":["https://openalex.org/I142740786"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":3.9863,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.93507501,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"10","issue":"S7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9301999807357788,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9301999807357788,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.043800000101327896,"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":0.007199999876320362,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pairwise-sequence-alignment","display_name":"pairwise sequence alignment","score":0.9879999756813049},{"id":"https://openalex.org/keywords/multiple-gpus","display_name":"multiple GPUs","score":0.6690000295639038},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.8059999942779541},{"id":"https://openalex.org/keywords/gpu-computing","display_name":"GPU computing","score":0.6740000247955322},{"id":"https://openalex.org/keywords/smith-waterman-algorithm","display_name":"Smith-Waterman algorithm","score":0.9259999990463257},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"dynamic programming","score":0.8769999742507935},{"id":"https://openalex.org/keywords/local-sequence-alignment","display_name":"local alignment","score":0.8859999775886536},{"id":"https://openalex.org/keywords/protein-sequence-comparison","display_name":"protein sequence comparison","score":0.6570000052452087},{"id":"https://openalex.org/keywords/dna-sequence-comparison","display_name":"DNA sequence comparison","score":0.9470000267028809},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"parallel computing","score":0.5870000123977661}],"concepts":[{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.844886302947998},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8215360641479492},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6956868171691895},{"id":"https://openalex.org/C86111242","wikidata":"https://www.wikidata.org/wiki/Q859595","display_name":"Coprocessor","level":2,"score":0.6736725568771362},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.6624378561973572},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.6471800208091736},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.6012718677520752},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.5722975134849548},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.5189363956451416},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5092507600784302},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4795648455619812},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.4468365013599396},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.41768038272857666},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.27060386538505554},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14829865097999573},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.12151163816452026},{"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},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-10-s7-a3","doi":"https://doi.org/10.1186/1471-2105-10-s7-a3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s7-a3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S7-A3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2318285","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3313266","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3313266","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3313266/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.270.805","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.270.805","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/7b/bb/BMC_Bioinformatics_2009_Jun_25_10(Suppl_7)_A3.tar.gz","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:d9931b951d444008b4830e5042c6f18d","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/d9931b951d444008b4830e5042c6f18d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss Suppl 7, p A3 (2009)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-s7-a3","doi":"https://doi.org/10.1186/1471-2105-10-s7-a3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s7-a3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S7-A3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2109268917.pdf","grobid_xml":"https://content.openalex.org/works/W2109268917.grobid-xml"},"referenced_works_count":1,"referenced_works":["https://openalex.org/W2087064593"],"related_works":["https://openalex.org/W7096811385","https://openalex.org/W4206226005","https://openalex.org/W2106074773","https://openalex.org/W2017639035","https://openalex.org/W2012129103","https://openalex.org/W2165949232","https://openalex.org/W7095736351","https://openalex.org/W144941342","https://openalex.org/W4391316571","https://openalex.org/W2789781797"],"abstract_inverted_index":{"Recently,":[0],"rapid":[1],"growth":[2],"of":[3,6,17,43,81,89,122,129,132],"the":[4,7,21,30,40,59,82,90,101,127,130,133,136,140,144],"technology":[5],"Graphics":[8],"Processing":[9],"Unit":[10],"(GPU)":[11],"has":[12,67],"led":[13],"to":[14,85,99,113,126,149],"a":[15,35,69,109,119,154,159],"surge":[16],"interest":[18],"in":[19,32,61],"using":[20],"GPU":[22,31,41,47],"for":[23,87,158],"general":[24],"purpose":[25],"applications.":[26],"We":[27],"can":[28],"utilize":[29],"computation":[33,123],"as":[34,153],"massive":[36],"parallel":[37],"coprocessor":[38],"because":[39],"consists":[42],"multiple":[44,145],"cores.":[45],"The":[46,72],"is":[48,79],"also":[49],"an":[50],"affordable,":[51],"user-programmable,":[52],"and":[53,63,138],"attractive":[54],"commodity.":[55],"In":[56],"bioinformatics,":[57],"finding":[58],"similarities":[60],"protein":[62],"DNA":[64],"sequence":[65],"databases":[66],"become":[68],"fundamental":[70],"procedure.":[71],"Smith-Waterman":[73],"algorithm":[74],"based":[75],"on":[76,139],"dynamic":[77,106],"programming":[78,107],"one":[80],"methods":[83],"used":[84],"search":[86],"all":[88],"possible":[91],"local":[92,103],"alignments":[93],"between":[94],"two":[95,134],"sequences,":[96],"enabling":[97],"us":[98],"find":[100],"optimal":[102],"alignments.":[104],"However,":[105],"requires":[108],"sequential":[110],"calculation":[111],"due":[112],"data":[114],"dependency.":[115],"Also":[116],"required":[117],"are":[118,147],"high":[120,155],"number":[121],"steps":[124],"proportional":[125],"product":[128],"lengths":[131],"sequences.":[135],"CPU":[137],"single":[141],"GPU.":[142],"Therefore,":[143],"GPUs":[146],"shown":[148],"be":[150],"extremely":[151],"efficient":[152],"computing":[156],"accelerator":[157],"bioinformatics":[160],"application.":[161]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":5}],"updated_date":"2026-11-11T12:16:26.678958","created_date":"2016-06-24T00:00:00"}