{"id":"https://openalex.org/W2160097763","doi":"https://doi.org/10.1186/1471-2105-9-377","title":"CBESW: Sequence Alignment on the Playstation 3","display_name":"CBESW: Sequence Alignment on the Playstation 3","publication_year":2008,"publication_date":"2008-09-17","ids":{"openalex":"https://openalex.org/W2160097763","doi":"https://doi.org/10.1186/1471-2105-9-377","mag":"2160097763","pmid":"https://pubmed.ncbi.nlm.nih.gov/18798993"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-377","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-377","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-377","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,"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"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-377","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074813540","display_name":"Adrianto Wirawan","orcid":null},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Adrianto Wirawan","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore. adri0004@ntu.edu.sg","School of Computer Engineering, Nanyang Technological University, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore. adri0004@ntu.edu.sg","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027208445","display_name":"Chee Keong Kwoh","orcid":"https://orcid.org/0000-0002-8547-6387"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Chee Keong Kwoh","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Nim Tri Hieu","orcid":null},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Nim Tri Hieu","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Bertil Schmidt","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5074813540"],"corresponding_institution_ids":["https://openalex.org/I172675005"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":3.1193,"has_fulltext":true,"cited_by_count":52,"citation_normalized_percentile":{"value":0.922275,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"9","issue":"1","first_page":"377","last_page":"377"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.676800012588501,"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":0.676800012588501,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.09239999949932098,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.06340000033378601,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5272150039672852},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5207112431526184},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.46781253814697266},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4632033109664917},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.41062772274017334},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3129061460494995},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2777141332626343},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.14890632033348083},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13974392414093018}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5272150039672852},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5207112431526184},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.46781253814697266},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4632033109664917},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.41062772274017334},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3129061460494995},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2777141332626343},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.14890632033348083},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13974392414093018}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018910","descriptor_name":"Video Games","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018910","descriptor_name":"Video Games","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018910","descriptor_name":"Video Games","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-9-377","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-377","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-377","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,"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":"pmid:18798993","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18798993","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"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":null},{"id":"pmh:oai:doaj.org/article:d8d935fd28ca4bbe86dbb28296ff039c","is_oa":false,"landing_page_url":"https://doaj.org/article/d8d935fd28ca4bbe86dbb28296ff039c","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,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss 1, p 377 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2571991","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2571991","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,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-377","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-377","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-377","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,"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":[{"display_name":"Industry, innovation and infrastructure","score":0.4399999976158142,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320766","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2160097763.pdf","grobid_xml":"https://content.openalex.org/works/W2160097763.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1558365920","https://openalex.org/W1586673205","https://openalex.org/W2006899413","https://openalex.org/W2009570821","https://openalex.org/W2011652244","https://openalex.org/W2059807497","https://openalex.org/W2068448872","https://openalex.org/W2087064593","https://openalex.org/W2089499735","https://openalex.org/W2116508956","https://openalex.org/W2122942724","https://openalex.org/W2132967231","https://openalex.org/W2133098231","https://openalex.org/W2146379626","https://openalex.org/W2152706101","https://openalex.org/W2155282902","https://openalex.org/W2164856315","https://openalex.org/W4205502579","https://openalex.org/W4245668478","https://openalex.org/W4247964656"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W1525517788","https://openalex.org/W3119443523","https://openalex.org/W2353952613"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,35,129],"exponential":[2],"growth":[3],"of":[4,38,123],"available":[5],"biological":[6],"data":[7],"has":[8,41],"caused":[9],"bioinformatics":[10,28,55],"to":[11,45,58,84,107,125],"be":[12,78,141],"rapidly":[13],"moving":[14],"towards":[15],"a":[16,21,81,100,120],"data-intensive,":[17],"computational":[18,24,82,148],"science.":[19],"As":[20],"result,":[22],"the":[23,68,73,86,96,136],"power":[25],"needed":[26],"by":[27,72],"applications":[29],"is":[30],"growing":[31],"exponentially":[32],"as":[33,80,111,143],"well.":[34],"recent":[36],"emergence":[37],"accelerator":[39],"technologies":[40],"made":[42],"it":[43],"possible":[44],"achieve":[46],"an":[47,144],"excellent":[48],"improvement":[49,102],"in":[50,103],"execution":[51],"time":[52,105],"for":[53,150],"many":[54],"applications,":[56],"compared":[57,106],"current":[59],"general-purpose":[60],"platforms.":[61],"In":[62],"this":[63],"paper,":[64],"we":[65],"demonstrate":[66,134],"how":[67],"PlayStation":[69,97,137],"3,":[70],"powered":[71],"Cell":[74],"Broadband":[75],"Engine,":[76],"can":[77,140],"used":[79,142],"platform":[83,149],"accelerate":[85],"Smith-Waterman":[87,114],"algorithm.":[88],"RESULTS:":[89],"For":[90],"large":[91],"datasets,":[92],"our":[93,132],"implementation":[94,118],"on":[95],"3":[98,138],"provides":[99],"significant":[101],"running":[104],"other":[108],"implementations":[109],"such":[110],"SSEARCH,":[112],"Striped":[113],"and":[115],"CUDA.":[116],"Our":[117],"achieves":[119],"peak":[121],"performance":[122,152],"up":[124],"3,646":[126],"MCUPS.":[127],"CONCLUSION:":[128],"results":[130],"from":[131],"experiments":[133],"that":[135],"console":[139],"efficient":[145],"low":[146],"cost":[147],"high":[151],"sequence":[153],"alignment":[154],"applications.":[155]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":4}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
