{"id":"https://openalex.org/W2096041635","doi":"https://doi.org/10.1093/bioinformatics/btq644","title":"GPU-BLAST: using graphics processors to accelerate protein sequence alignment","display_name":"GPU-BLAST: using graphics processors to accelerate protein sequence alignment","publication_year":2010,"publication_date":"2010-11-18","ids":{"openalex":"https://openalex.org/W2096041635","doi":"https://doi.org/10.1093/bioinformatics/btq644","mag":"2096041635","pmid":"https://pubmed.ncbi.nlm.nih.gov/21088027"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq644","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq644","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/2/182/48867571/bioinformatics_27_2_182.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/2/182/48867571/bioinformatics_27_2_182.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044424866","display_name":"Panagiotis D. Vouzis","orcid":null},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Panagiotis D. Vouzis","raw_affiliation_strings":["1 Department of Chemical Engineering and 2Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Chemical Engineering and 2Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031811254","display_name":"Nikolaos V. Sahinidis","orcid":"https://orcid.org/0000-0003-2087-9131"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nikolaos V. Sahinidis","raw_affiliation_strings":["1 Department of Chemical Engineering and 2Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Chemical Engineering and 2Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":6.3984,"has_fulltext":true,"cited_by_count":213,"citation_normalized_percentile":{"value":0.9742503,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"27","issue":"2","first_page":"182","last_page":"188"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.43630000948905945,"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":0.43630000948905945,"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":0.302700012922287,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.0551999993622303,"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/computer-science","display_name":"Computer science","score":0.7833529114723206},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.6354345083236694},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.6162165999412537},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.6159319281578064},{"id":"https://openalex.org/keywords/air-blast","display_name":"Air blast","score":0.6032077670097351},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5223223567008972},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5118681788444519},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5032715201377869},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3203292489051819},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.25478774309158325},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.24984809756278992}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7833529114723206},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.6354345083236694},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.6162165999412537},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.6159319281578064},{"id":"https://openalex.org/C2994289025","wikidata":"https://www.wikidata.org/wiki/Q4114774","display_name":"Air blast","level":2,"score":0.6032077670097351},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5223223567008972},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5118681788444519},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5032715201377869},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3203292489051819},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.25478774309158325},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.24984809756278992},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C16674752","wikidata":"https://www.wikidata.org/wiki/Q1370637","display_name":"Mining engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btq644","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq644","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/2/182/48867571/bioinformatics_27_2_182.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21088027","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21088027","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3018811","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3018811","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.890.173","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.890.173","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2010/11/17/bioinformatics.btq644.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.895.3619","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.895.3619","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/27/2/182.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq644","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq644","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/2/182/48867571/bioinformatics_27_2_182.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2096041635.pdf","grobid_xml":"https://content.openalex.org/works/W2096041635.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W21816278","https://openalex.org/W1547749660","https://openalex.org/W1595749330","https://openalex.org/W1898130445","https://openalex.org/W1991001523","https://openalex.org/W1991297274","https://openalex.org/W2011652244","https://openalex.org/W2043198910","https://openalex.org/W2055043387","https://openalex.org/W2072177669","https://openalex.org/W2075849238","https://openalex.org/W2087064593","https://openalex.org/W2088481815","https://openalex.org/W2094519647","https://openalex.org/W2111609443","https://openalex.org/W2124677924","https://openalex.org/W2136485386","https://openalex.org/W2142678478","https://openalex.org/W2143210482","https://openalex.org/W2150056503","https://openalex.org/W2158714788","https://openalex.org/W2162041888","https://openalex.org/W2163809936","https://openalex.org/W2166621589","https://openalex.org/W2184317164","https://openalex.org/W2911830835","https://openalex.org/W4238383811","https://openalex.org/W6648144904","https://openalex.org/W6648329412","https://openalex.org/W6683565055"],"related_works":["https://openalex.org/W2119534391","https://openalex.org/W1966576946","https://openalex.org/W2503137108","https://openalex.org/W2023770367","https://openalex.org/W2062253548","https://openalex.org/W2393490604","https://openalex.org/W2393707426","https://openalex.org/W2030707850","https://openalex.org/W2146871484","https://openalex.org/W2794923745"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,17,100,140],"Basic":[2],"Local":[3],"Alignment":[4],"Search":[5],"Tool":[6],"(BLAST)":[7],"is":[8,22,102,145],"one":[9],"of":[10,20,41,59,63,69,78,96,108,143],"the":[11,34,39,42,56,67,97,105,112,125,128],"most":[12],"widely":[13],"used":[14],"bioinformatics":[15],"tools.":[16],"widespread":[18],"impact":[19],"BLAST":[21,60],"reflected":[23],"in":[24,33,55,66],"over":[25],"53,000":[26],"citations":[27],"that":[28],"this":[29],"software":[30],"has":[31],"received":[32],"past":[35],"two":[36],"decades,":[37],"and":[38,71,115,137],"use":[40],"word":[43],"'blast'":[44],"as":[45],"a":[46,83],"verb":[47],"referring":[48],"to":[49,124],"biological":[50],"sequence":[51],"comparison.":[52],"Any":[53],"improvement":[54],"execution":[57],"speed":[58],"would":[61],"be":[62],"great":[64],"importance":[65],"practice":[68],"bioinformatics,":[70],"facilitate":[72],"coping":[73],"with":[74],"ever":[75],"increasing":[76],"sizes":[77],"biomolecular":[79],"databases.":[80],"RESULTS:":[81],"Using":[82],"general-purpose":[84],"graphics":[85],"processing":[86],"unit":[87],"(GPU),":[88],"we":[89],"have":[90],"developed":[91],"GPU-BLAST,":[92],"an":[93],"accelerated":[94],"version":[95],"popular":[98],"NCBI-BLAST.":[99],"implementation":[101],"based":[103],"on":[104],"source":[106,141],"code":[107,142],"NCBI-BLAST,":[109,127],"thus":[110],"maintaining":[111],"same":[113],"input":[114],"output":[116],"interface":[117],"while":[118],"producing":[119],"identical":[120],"results.":[121],"In":[122],"comparison":[123],"sequential":[126],"speedups":[129],"achieved":[130],"by":[131],"GPU-BLAST":[132,144],"range":[133],"mostly":[134],"between":[135],"3":[136],"4.":[138],"AVAILABILITY:":[139],"freely":[146],"available":[147],"at":[148],"http://archimedes.cheme.cmu.edu/biosoftware.html.":[149]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":13},{"year":2018,"cited_by_count":17},{"year":2017,"cited_by_count":21},{"year":2016,"cited_by_count":18},{"year":2015,"cited_by_count":24},{"year":2014,"cited_by_count":20},{"year":2013,"cited_by_count":23},{"year":2012,"cited_by_count":16}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
