{"id":"https://openalex.org/W3169838823","doi":"https://doi.org/10.1109/tpds.2021.3084069","title":"Parallel Fine-Grained Comparison of Long DNA Sequences in Homogeneous and Heterogeneous GPU Platforms With Pruning","display_name":"Parallel Fine-Grained Comparison of Long DNA Sequences in Homogeneous and Heterogeneous GPU Platforms With Pruning","publication_year":2021,"publication_date":"2021-05-26","ids":{"openalex":"https://openalex.org/W3169838823","doi":"https://doi.org/10.1109/tpds.2021.3084069","mag":"3169838823"},"language":"en","primary_location":{"id":"doi:10.1109/tpds.2021.3084069","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tpds.2021.3084069","pdf_url":null,"source":{"id":"https://openalex.org/S97130795","display_name":"IEEE Transactions on Parallel and Distributed Systems","issn_l":"1045-9219","issn":["1045-9219","1558-2183","2161-9883"],"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 Transactions on Parallel and Distributed Systems","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/A5079507770","display_name":"Marco Figueiredo","orcid":"https://orcid.org/0000-0003-0039-310X"},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Marco Figueiredo","raw_affiliation_strings":["University of Brasilia, Brasilia, Brazil"],"raw_orcid":"https://orcid.org/0000-0003-0039-310X","affiliations":[{"raw_affiliation_string":"University of Brasilia, Brasilia, Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068263812","display_name":"Jo\u00e3o Paulo Navarro","orcid":"https://orcid.org/0000-0001-7878-2944"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Joao Paulo Navarro","raw_affiliation_strings":["NVidia, Sao Paulo, Brazil"],"raw_orcid":"https://orcid.org/0000-0001-7878-2944","affiliations":[{"raw_affiliation_string":"NVidia, Sao Paulo, Brazil","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058639233","display_name":"Edans F. O. Sandes","orcid":"https://orcid.org/0000-0001-9502-7799"},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Edans F. O. Sandes","raw_affiliation_strings":["University of Brasilia, Brasilia, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Brasilia, Brasilia, Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076465098","display_name":"George Teodoro","orcid":"https://orcid.org/0000-0001-6289-3914"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"George Teodoro","raw_affiliation_strings":["Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universidade Federal de Minas Gerais, Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005717412","display_name":"Alba Cristina Magalh\u00e3es Alves de Melo","orcid":"https://orcid.org/0000-0001-5191-5209"},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Alba C. M. A. Melo","raw_affiliation_strings":["University of Brasilia, Brasilia, Brazil"],"raw_orcid":"https://orcid.org/0000-0001-5191-5209","affiliations":[{"raw_affiliation_string":"University of Brasilia, Brasilia, Brazil","institution_ids":["https://openalex.org/I150729083"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6514,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.66676422,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"32","issue":"12","first_page":"3053","last_page":"3065"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9991000294685364,"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":0.996999979019165,"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/T11482","display_name":"RNA modifications and cancer","score":0.9926000237464905,"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":0.874021589756012},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7856005430221558},{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.7700987458229065},{"id":"https://openalex.org/keywords/homogeneous","display_name":"Homogeneous","score":0.6574460864067078},{"id":"https://openalex.org/keywords/workload","display_name":"Workload","score":0.5794793963432312},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4755629897117615},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.47373688220977783},{"id":"https://openalex.org/keywords/block","display_name":"Block (permutation group theory)","score":0.4679027497768402},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.4272405803203583},{"id":"https://openalex.org/keywords/gpu-cluster","display_name":"GPU cluster","score":0.42173996567726135},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.3399868607521057},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2607692778110504},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.10547783970832825}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.874021589756012},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7856005430221558},{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.7700987458229065},{"id":"https://openalex.org/C66882249","wikidata":"https://www.wikidata.org/wiki/Q169336","display_name":"Homogeneous","level":2,"score":0.6574460864067078},{"id":"https://openalex.org/C2778476105","wikidata":"https://www.wikidata.org/wiki/Q628539","display_name":"Workload","level":2,"score":0.5794793963432312},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4755629897117615},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.47373688220977783},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.4679027497768402},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.4272405803203583},{"id":"https://openalex.org/C2781335571","wikidata":"https://www.wikidata.org/wiki/Q2633544","display_name":"GPU cluster","level":3,"score":0.42173996567726135},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.3399868607521057},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2607692778110504},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.10547783970832825},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"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/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","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/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tpds.2021.3084069","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tpds.2021.3084069","pdf_url":null,"source":{"id":"https://openalex.org/S97130795","display_name":"IEEE Transactions on Parallel and Distributed Systems","issn_l":"1045-9219","issn":["1045-9219","1558-2183","2161-9883"],"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 Transactions on Parallel and Distributed Systems","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W55643954","https://openalex.org/W1592614241","https://openalex.org/W1979984357","https://openalex.org/W1986228396","https://openalex.org/W1995106824","https://openalex.org/W1997543791","https://openalex.org/W2002719872","https://openalex.org/W2013733655","https://openalex.org/W2017972683","https://openalex.org/W2021342241","https://openalex.org/W2046220835","https://openalex.org/W2057998009","https://openalex.org/W2061996139","https://openalex.org/W2065461987","https://openalex.org/W2068448872","https://openalex.org/W2074231493","https://openalex.org/W2079900503","https://openalex.org/W2087064593","https://openalex.org/W2098232690","https://openalex.org/W2103914320","https://openalex.org/W2108215151","https://openalex.org/W2108317509","https://openalex.org/W2131456947","https://openalex.org/W2140917900","https://openalex.org/W2146379626","https://openalex.org/W2147865717","https://openalex.org/W2165654401","https://openalex.org/W2285697638","https://openalex.org/W2344543892","https://openalex.org/W2471092755","https://openalex.org/W2599597882","https://openalex.org/W2724179501","https://openalex.org/W2753396470","https://openalex.org/W2762987563","https://openalex.org/W2789843538","https://openalex.org/W2799394118","https://openalex.org/W2971413258","https://openalex.org/W3025150241","https://openalex.org/W3032041425","https://openalex.org/W3084730237","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W3165899388","https://openalex.org/W1445273741","https://openalex.org/W4288452443","https://openalex.org/W2108266785","https://openalex.org/W2030707850","https://openalex.org/W2346107805","https://openalex.org/W2965037703","https://openalex.org/W2133684822","https://openalex.org/W2562576480","https://openalex.org/W1955619021"],"abstract_inverted_index":{"The":[0,123],"parallelization":[1],"of":[2,23,32,41,162,185,189],"Smith-Waterman":[3],"(SW)":[4],"sequence":[5,48],"comparison":[6,49,161],"tools":[7,204],"for":[8,202],"long":[9],"DNA":[10],"sequences":[11],"has":[12],"been":[13],"a":[14,47,83,170],"big":[15],"challenge":[16],"over":[17],"the":[18,21,39,70,73,87,102,136,153,160,163,182,199],"years,":[19],"requesting":[20],"use":[22],"several":[24],"devices":[25],"and":[26,72,95,111,115,129,138,165,180],"sophisticated":[27],"optimizations.":[28],"Pruning":[29],"is":[30,66,76,91,97,149],"one":[31],"these":[33],"optimizations,":[34],"which":[35,194],"can":[36],"reduce":[37],"considerably":[38],"amount":[40],"computation.":[42],"This":[43],"article":[44],"proposes":[45],"MultiBP,":[46],"solution":[50],"in":[51,113,126,156,169,205],"multiple":[52],"GPUs":[53,80,103,176],"with":[54,118,172],"block":[55],"pruning.":[56],"Two":[57],"MultiBP":[58,106],"strategies":[59],"are":[60],"proposed.":[61],"In":[62,86],"static":[63,137],"score-sharing,":[64],"workload":[65,96],"statically":[67],"distributed":[68],"to":[69,78,81,101,109,151,196],"GPUs,":[71],"best":[74,124,154,200],"score":[75],"sent":[77],"neighbor":[79],"simulate":[82],"global":[84],"view.":[85],"dynamic":[88,139],"strategy,":[89],"execution":[90],"divided":[92],"into":[93],"cycles":[94],"dynamically":[98],"assigned,":[99],"according":[100],"processing":[104],"rate.":[105],"was":[107],"integrated":[108],"MASA-CUDAlign":[110],"tested":[112],"homogeneous":[114,128],"heterogeneous":[116,130],"platforms,":[117],"different":[119],"NVidia":[120,175],"GPU":[121],"architectures.":[122],"results":[125],"our":[127,146,197],"platforms":[131],"were":[132],"mostly":[133],"obtained":[134,181],"by":[135],"approaches,":[140],"respectively.":[141],"We":[142],"also":[143],"show":[144],"that":[145],"decision":[147],"module":[148],"able":[150],"select":[152],"strategy":[155],"most":[157],"cases.":[158],"Finally,":[159],"human":[164],"chimpanzee":[166],"chromosomes":[167],"1":[168],"cluster":[171],"512":[173],"V100":[174],"took":[177],"11":[178],"minutes":[179],"impressive":[183],"rate":[184],"82,822":[186],"GCUPS":[187],"(Billions":[188],"Cells":[190],"Updated":[191],"per":[192],"Second)":[193],"is,":[195],"knowledge,":[198],"performance":[201],"SW":[203],"GPUs.":[206]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
