{"id":"https://openalex.org/W2422616509","doi":"https://doi.org/10.1109/tcbb.2015.2489662","title":"cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on CPU+GPU","display_name":"cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on CPU+GPU","publication_year":2015,"publication_date":"2015-10-13","ids":{"openalex":"https://openalex.org/W2422616509","doi":"https://doi.org/10.1109/tcbb.2015.2489662","mag":"2422616509"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2015.2489662","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2489662","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","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/A5061841494","display_name":"Jing Zhang","orcid":"https://orcid.org/0000-0002-8495-2804"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jing Zhang","raw_affiliation_strings":["Department of Computer Science, Virginia Tech 225 Stanger Street, Blacksburg, VA 24061"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech 225 Stanger Street, Blacksburg, VA 24061","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100446064","display_name":"Hao Wang","orcid":"https://orcid.org/0000-0001-9301-5989"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hao Wang","raw_affiliation_strings":["Department of Computer Science, Virginia Tech 225 Stanger Street, Blacksburg, VA 24061"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech 225 Stanger Street, Blacksburg, VA 24061","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058539554","display_name":"Wu-chun Feng","orcid":"https://orcid.org/0000-0002-6015-0727"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wu-chun Feng","raw_affiliation_strings":["Department of Computer Science, Virginia Tech 225 Stanger Street, Blacksburg, VA 24061"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech 225 Stanger Street, Blacksburg, VA 24061","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5061841494"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":2.4145,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.89430553,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"14","issue":"4","first_page":"830","last_page":"843"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9945999979972839,"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":0.9824000000953674,"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":0.8553096652030945},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7502448558807373},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7268880009651184},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.6060574650764465},{"id":"https://openalex.org/keywords/thread","display_name":"Thread (computing)","score":0.5942810773849487},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.5359085202217102},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.522529125213623},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.5056023597717285},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.49283552169799805},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.4885757863521576},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.44940489530563354},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.2076350748538971},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.07975888252258301}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8553096652030945},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7502448558807373},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7268880009651184},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.6060574650764465},{"id":"https://openalex.org/C138101251","wikidata":"https://www.wikidata.org/wiki/Q213092","display_name":"Thread (computing)","level":2,"score":0.5942810773849487},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.5359085202217102},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.522529125213623},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.5056023597717285},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.49283552169799805},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.4885757863521576},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.44940489530563354},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.2076350748538971},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.07975888252258301},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2015.2489662","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2489662","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/76659","is_oa":false,"landing_page_url":"http://hdl.handle.net/10919/76659","pdf_url":null,"source":{"id":"https://openalex.org/S4306400248","display_name":"VTechWorks (Virginia Tech)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I859038795","host_organization_name":"Virginia Tech","host_organization_lineage":["https://openalex.org/I859038795"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Responsible consumption and production","id":"https://metadata.un.org/sdg/12","score":0.5199999809265137}],"awards":[{"id":"https://openalex.org/G2251738032","display_name":"MRI-R2: Acquisition of a Heterogeneous Supercomputing Instrument for Transformative Interdisciplinary Research","funder_award_id":"0960081","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3666695478","display_name":null,"funder_award_id":"BIGDATA","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5808022030","display_name":"BIGDATA: Mid-Scale: DA: Collaborative Research: Genomes Galore - Core Techniques, Libraries, and Domain Specific Languages for High-Throughput DNA Sequencing","funder_award_id":"1247693","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6986638558","display_name":null,"funder_award_id":"IIS-1247693","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G988095577","display_name":null,"funder_award_id":"CNS-0960081","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309646","display_name":"Virginia Polytechnic Institute and State University","ror":"https://ror.org/02smfhw86"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W145805655","https://openalex.org/W406435780","https://openalex.org/W1978885894","https://openalex.org/W2055043387","https://openalex.org/W2057496513","https://openalex.org/W2057783089","https://openalex.org/W2072177669","https://openalex.org/W2087064593","https://openalex.org/W2091450837","https://openalex.org/W2096041635","https://openalex.org/W2103644816","https://openalex.org/W2104262506","https://openalex.org/W2115036455","https://openalex.org/W2122482436","https://openalex.org/W2128964206","https://openalex.org/W2136145671","https://openalex.org/W2142619120","https://openalex.org/W2142678478","https://openalex.org/W2155957132","https://openalex.org/W2156137607","https://openalex.org/W2158714788","https://openalex.org/W2159742629","https://openalex.org/W2163932369","https://openalex.org/W2168938595","https://openalex.org/W2171474230","https://openalex.org/W2377704851","https://openalex.org/W4236236547","https://openalex.org/W4241407634","https://openalex.org/W4247927165","https://openalex.org/W4285719527","https://openalex.org/W6614066585"],"related_works":["https://openalex.org/W2023938924","https://openalex.org/W3045090683","https://openalex.org/W2755264124","https://openalex.org/W2130748128","https://openalex.org/W14969471","https://openalex.org/W3023773069","https://openalex.org/W84129006","https://openalex.org/W2536676298","https://openalex.org/W2008492897","https://openalex.org/W2170268965"],"abstract_inverted_index":{"BLAST,":[0],"short":[1],"for":[2,17,66],"Basic":[3],"Local":[4],"Alignment":[5],"Search":[6],"Tool,":[7],"is":[8,43,81,133],"a":[9,97,120,139,183],"ubiquitous":[10],"tool":[11],"used":[12],"in":[13,106],"the":[14,23,31,37,49,56,63,94,102,115,157,171,191,195],"life":[15],"sciences":[16],"pairwise":[18],"sequence":[19,41,79,131],"search.":[20],"However,":[21],"with":[22,179,190],"advent":[24],"of":[25,40,96,104,130,156],"next-generation":[26],"sequencing":[27],"(NGS),":[28],"whether":[29],"at":[30],"outset":[32],"or":[33],"downstream":[34],"from":[35],"NGS,":[36],"exponential":[38],"growth":[39],"databases":[42],"outstripping":[44],"our":[45],"ability":[46],"to":[47,61,83,101,123,135,146],"analyze":[48],"data.":[50],"While":[51],"recent":[52],"studies":[53,73],"have":[54],"utilized":[55],"graphics":[57],"processing":[58],"unit":[59],"(GPU)":[60],"speedup":[62],"BLAST":[64],"algorithm":[65],"searching":[67],"protein":[68],"sequences":[69],"(i.e.,":[70,161,174],"BLASTP),":[71],"these":[72],"use":[74],"coarse-grained":[75],"parallelism,":[76],"where":[77,126],"one":[78,85],"alignment":[80,178],"mapped":[82,134],"only":[84],"thread.":[86],"Such":[87],"an":[88],"approach":[89,122],"does":[90],"not":[91],"efficiently":[92],"utilize":[93],"capabilities":[95],"GPU,":[98],"particularly":[99],"due":[100],"irregularity":[103],"BLASTP":[105],"both":[107],"execution":[108,189],"paths":[109],"and":[110,152,164,177,186],"memory-access":[111],"patterns.":[112],"To":[113],"address":[114],"above":[116],"shortcomings,":[117],"we":[118,144],"present":[119],"fine-grained":[121],"parallelize":[124],"BLASTP,":[125],"each":[127],"individual":[128],"phase":[129],"search":[132],"many":[136],"threads":[137],"on":[138,182,194],"GPU.":[140,196],"This":[141],"approach,":[142],"which":[143],"refer":[145],"as":[147],"cuBLASTP,":[148],"reorders":[149],"data-access":[150],"patterns":[151],"reduces":[153],"divergent":[154],"branches":[155],"most":[158],"time-consuming":[159],"phases":[160,173,192],"hit":[162],"detection":[163],"ungapped":[165],"extension).":[166],"In":[167],"addition,":[168],"cuBLASTP":[169],"optimizes":[170],"remaining":[172],"gapped":[175],"extension":[176],"trace":[180],"back)":[181],"multicore":[184],"CPU":[185],"overlaps":[187],"their":[188],"running":[193]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2016-06-24T00:00:00"}