{"id":"https://openalex.org/W2084018711","doi":"https://doi.org/10.1145/1242531.1242542","title":"Parallel genomic sequence-search on a massively parallel system","display_name":"Parallel genomic sequence-search on a massively parallel system","publication_year":2007,"publication_date":"2007-05-07","ids":{"openalex":"https://openalex.org/W2084018711","doi":"https://doi.org/10.1145/1242531.1242542","mag":"2084018711"},"language":"en","primary_location":{"id":"doi:10.1145/1242531.1242542","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1242531.1242542","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 4th international conference on Computing frontiers","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/A5088155465","display_name":"Oystein Thorsen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120349","display_name":"University of Minnesota Rochester","ror":"https://ror.org/02rh4fw73","country_code":"US","type":"education","lineage":["https://openalex.org/I4210120349"]},{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Oystein Thorsen","raw_affiliation_strings":["IBM - Rochester, Rochester, MN","IBM - Rochester, Rochester, MN#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM - Rochester, Rochester, MN","institution_ids":["https://openalex.org/I4210120349"]},{"raw_affiliation_string":"IBM - Rochester, Rochester, MN#TAB#","institution_ids":["https://openalex.org/I5388228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108675267","display_name":"Brian Smith","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120349","display_name":"University of Minnesota Rochester","ror":"https://ror.org/02rh4fw73","country_code":"US","type":"education","lineage":["https://openalex.org/I4210120349"]},{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian Smith","raw_affiliation_strings":["IBM - Rochester, Rochester, MN","IBM - Rochester, Rochester, MN#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM - Rochester, Rochester, MN","institution_ids":["https://openalex.org/I4210120349"]},{"raw_affiliation_string":"IBM - Rochester, Rochester, MN#TAB#","institution_ids":["https://openalex.org/I5388228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109958670","display_name":"Carlos P. Sosa","orcid":null},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carlos P. Sosa","raw_affiliation_strings":["University of Minnesota, Minneapolis, MN","University of Minnesota , Minneapolis, Mn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Minnesota, Minneapolis, MN","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"University of Minnesota , Minneapolis, Mn","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038161074","display_name":"Karl Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120349","display_name":"University of Minnesota Rochester","ror":"https://ror.org/02rh4fw73","country_code":"US","type":"education","lineage":["https://openalex.org/I4210120349"]},{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karl Jiang","raw_affiliation_strings":["IBM - Rochester, Rochester, MN","IBM - Rochester, Rochester, MN#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM - Rochester, Rochester, MN","institution_ids":["https://openalex.org/I4210120349"]},{"raw_affiliation_string":"IBM - Rochester, Rochester, MN#TAB#","institution_ids":["https://openalex.org/I5388228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103124804","display_name":"Heshan Lin","orcid":"https://orcid.org/0000-0003-0825-6169"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Heshan Lin","raw_affiliation_strings":["North Carolina State University, Raleigh, NC","North Carolina State University, Raleigh, NC;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"North Carolina State University, Raleigh, NC","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"North Carolina State University, Raleigh, NC;","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112710952","display_name":"Amanda Peters","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120349","display_name":"University of Minnesota Rochester","ror":"https://ror.org/02rh4fw73","country_code":"US","type":"education","lineage":["https://openalex.org/I4210120349"]},{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amanda Peters","raw_affiliation_strings":["IBM - Rochester, Rochester, MN","IBM - Rochester, Rochester, MN#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM - Rochester, Rochester, MN","institution_ids":["https://openalex.org/I4210120349"]},{"raw_affiliation_string":"IBM - Rochester, Rochester, MN#TAB#","institution_ids":["https://openalex.org/I5388228"]}]},{"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":["Virginia Tech, Blacksburg, VA","Virginia Tech , Blacksburg, VA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Tech, Blacksburg, VA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Virginia Tech , Blacksburg, VA","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.6919,"has_fulltext":false,"cited_by_count":46,"citation_normalized_percentile":{"value":0.90218241,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"59","last_page":"68"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9990000128746033,"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/T10885","display_name":"Gene expression and cancer classification","score":0.96670001745224,"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/massively-parallel","display_name":"Massively parallel","score":0.8478795886039734},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7972749471664429},{"id":"https://openalex.org/keywords/ibm","display_name":"IBM","score":0.6313834190368652},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5807403326034546},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5258118510246277},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.5140234231948853},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.48520877957344055},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.4631836414337158},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09667560458183289},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.0880633294582367}],"concepts":[{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.8478795886039734},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7972749471664429},{"id":"https://openalex.org/C70388272","wikidata":"https://www.wikidata.org/wiki/Q5968558","display_name":"IBM","level":2,"score":0.6313834190368652},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5807403326034546},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5258118510246277},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.5140234231948853},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.48520877957344055},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.4631836414337158},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09667560458183289},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0880633294582367},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"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/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1242531.1242542","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1242531.1242542","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 4th international conference on Computing frontiers","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/12","score":0.5400000214576721,"display_name":"Responsible consumption and production"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W145805655","https://openalex.org/W170980215","https://openalex.org/W1978132986","https://openalex.org/W1985928578","https://openalex.org/W2055043387","https://openalex.org/W2103644816","https://openalex.org/W2109982223","https://openalex.org/W2112286591","https://openalex.org/W2125062675","https://openalex.org/W2134680739","https://openalex.org/W2153397025","https://openalex.org/W2155957132","https://openalex.org/W2156137607","https://openalex.org/W2158378903","https://openalex.org/W2158714788","https://openalex.org/W2917064891","https://openalex.org/W4244818997"],"related_works":["https://openalex.org/W3126131865","https://openalex.org/W2044344400","https://openalex.org/W4253186488","https://openalex.org/W1996938127","https://openalex.org/W2043380045","https://openalex.org/W2732495365","https://openalex.org/W4231814374","https://openalex.org/W2099557065","https://openalex.org/W2484410460","https://openalex.org/W2250278543"],"abstract_inverted_index":{"In":[0,162],"the":[1,41,50,68,72,108,111,181],"life":[2],"sciences,":[3],"genomic":[4],"databases":[5,24,185],"for":[6,37,53,201],"sequence":[7],"search":[8,22,39],"have":[9,85,166],"been":[10],"growing":[11],"exponentially":[12,75],"in":[13,61,77],"size.":[14,78],"As":[15],"a":[16,98,120,134,146,150,175,202],"result,":[17],"faster":[18],"sequence-search":[19],"algorithms":[20],"to":[21,26,28,87,110,119,133,187],"these":[23],"continue":[25],"evolve":[27],"cope":[29],"with":[30,67,177],"algorithmic":[31,59],"time":[32],"complexity.":[33],"The":[34,91,143,194],"ubiquitous":[35],"tool":[36],"such":[38,82,94],"is":[40,74],"Basic":[42],"Local":[43],"Alignment":[44],"Search":[45],"Tool":[46],"(BLAST)":[47],"[1]":[48],"from":[49],"National":[51],"Center":[52],"Biotechnology":[54],"Information":[55],"(NCBI).":[56],"Despite":[57],"continued":[58],"improvements":[60],"BLAST,":[62],"it":[63,131],"cannot":[64],"keep":[65],"up":[66],"rate":[69],"at":[70],"which":[71],"database":[73],"increasing":[76],"Therefore,":[79],"parallel":[80,121,136,204],"implement-ations":[81],"as":[83],"mpiBLAST":[84],"emerged":[86],"address":[88],"this":[89,163],"problem.":[90],"performance":[92],"of":[93,100,107,125],"implementations":[95],"depends":[96],"on":[97,172],"myriad":[99],"factors":[101],"including":[102],"algorithmic,":[103],"architectural,":[104],"and":[105,117,122,129,158,180,183],"mapping":[106],"algorithm":[109],"architecture.":[112],"This":[113],"paper":[114],"describes":[115],"modifications":[116],"extensions":[118,144],"distributed-memory":[123],"version":[124],"BLAST":[126],"called":[127],"mpiBLAST-PIO":[128,171],"how":[130],"maps":[132],"massively":[135,203],"system,":[137],"specifically":[138],"IBM":[139],"Blue":[140],"Gene/L":[141],"(BG/L).":[142],"include":[145],"virtual":[147],"file":[148],"manager,":[149],"\"multiple":[151],"master\"":[152],"run-time":[153],"model,":[154],"efficient":[155],"fragment":[156],"distribution,":[157],"intelligent":[159],"load":[160],"balancing.":[161],"study,":[164],"we":[165],"shown":[167],"that":[168],"our":[169],"optimized":[170],"BG/L":[173],"using":[174],"query":[176],"28014":[178],"sequences":[179],"NR":[182],"NT":[184],"scales":[186],"8192":[188],"nodes":[189],"(two":[190],"cores":[191],"per":[192],"node).":[193],"cases":[195],"tested":[196],"here":[197],"are":[198],"well":[199],"suited":[200],"system.":[205]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}