{"id":"https://openalex.org/W2015796252","doi":"https://doi.org/10.1109/padsw.2014.7097838","title":"Parallel exact spliced alignment on GPU","display_name":"Parallel exact spliced alignment on GPU","publication_year":2014,"publication_date":"2014-12-01","ids":{"openalex":"https://openalex.org/W2015796252","doi":"https://doi.org/10.1109/padsw.2014.7097838","mag":"2015796252"},"language":"en","primary_location":{"id":"doi:10.1109/padsw.2014.7097838","is_oa":false,"landing_page_url":"https://doi.org/10.1109/padsw.2014.7097838","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 20th IEEE International Conference on Parallel and Distributed Systems (ICPADS)","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/A5016108939","display_name":"Anisio Nolasco","orcid":null},"institutions":[{"id":"https://openalex.org/I122558511","display_name":"Universidade Federal de Mato Grosso do Sul","ror":"https://ror.org/0366d2847","country_code":"BR","type":"education","lineage":["https://openalex.org/I122558511"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Anisio Nolasco","raw_affiliation_strings":["School of Computing, Federal University of Mato Grosso do Sul, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, Federal University of Mato Grosso do Sul, Brazil","institution_ids":["https://openalex.org/I122558511"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070434727","display_name":"Nahri Moreano","orcid":"https://orcid.org/0000-0001-8305-4677"},"institutions":[{"id":"https://openalex.org/I122558511","display_name":"Universidade Federal de Mato Grosso do Sul","ror":"https://ror.org/0366d2847","country_code":"BR","type":"education","lineage":["https://openalex.org/I122558511"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Nahri Moreano","raw_affiliation_strings":["School of Computing, Federal University of Mato Grosso do Sul, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, Federal University of Mato Grosso do Sul, Brazil","institution_ids":["https://openalex.org/I122558511"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I122558511"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07509496,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"14","issue":null,"first_page":"426","last_page":"435"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994000196456909,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.996999979019165,"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":0.813003659248352},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6807225346565247},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.6765288710594177},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5442654490470886},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4778130352497101},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.47673356533050537},{"id":"https://openalex.org/keywords/data-parallelism","display_name":"Data parallelism","score":0.45858997106552124},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.4577961564064026},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4515012800693512},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.4277365803718567},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36338961124420166},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.15746399760246277}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.813003659248352},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6807225346565247},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.6765288710594177},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5442654490470886},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4778130352497101},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.47673356533050537},{"id":"https://openalex.org/C61483411","wikidata":"https://www.wikidata.org/wiki/Q3124522","display_name":"Data parallelism","level":3,"score":0.45858997106552124},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.4577961564064026},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4515012800693512},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.4277365803718567},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36338961124420166},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.15746399760246277},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/padsw.2014.7097838","is_oa":false,"landing_page_url":"https://doi.org/10.1109/padsw.2014.7097838","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 20th IEEE International Conference on Parallel and Distributed Systems (ICPADS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W993947271","https://openalex.org/W1533534862","https://openalex.org/W1543636183","https://openalex.org/W1762731526","https://openalex.org/W1844250772","https://openalex.org/W2000730583","https://openalex.org/W2077745293","https://openalex.org/W2105672886","https://openalex.org/W2115965694","https://openalex.org/W2123179625","https://openalex.org/W2154240181","https://openalex.org/W2162889091","https://openalex.org/W2164824418","https://openalex.org/W2165654401","https://openalex.org/W2168138800","https://openalex.org/W2225301576","https://openalex.org/W2259938310","https://openalex.org/W2398736067","https://openalex.org/W2993222596","https://openalex.org/W6625770492"],"related_works":["https://openalex.org/W2983282793","https://openalex.org/W1973046741","https://openalex.org/W2950520577","https://openalex.org/W1554644772","https://openalex.org/W2003935582","https://openalex.org/W2494130044","https://openalex.org/W3170887803","https://openalex.org/W2963831937","https://openalex.org/W74409296","https://openalex.org/W3209384898"],"abstract_inverted_index":{"Due":[0],"to":[1,28,33,68,74,87,103,110,139,168],"the":[2,29,50,58,69,82,91,131,135,149,154,158,185],"exponential":[3],"growth":[4],"of":[5,44,60,84,134,148,156,160],"biological":[6,150],"DNA":[7],"sequence":[8],"databases,":[9],"some":[10],"parallel":[11,26,173],"gene":[12,34,75],"prediction":[13,35],"solutions":[14,27,46],"on":[15],"different":[16],"high":[17],"performance":[18,116,179],"platforms":[19],"have":[20,39],"been":[21,40],"proposed.":[22],"Nevertheless,":[23],"few":[24],"exact":[25,66],"spliced":[30,70,92],"alignment":[31,71,93],"problem":[32,72],"in":[36,90,137,164],"eukaryotic":[37],"organisms":[38],"proposed":[41],"and":[42,105,175],"none":[43],"these":[45],"use":[47],"GPUs":[48],"as":[49],"target":[51],"platform.":[52],"In":[53],"this":[54],"paper,":[55],"we":[56],"present":[57],"development":[59],"two":[61,85,96],"GPU":[62,97],"accelerators":[63,98,115,136,186],"for":[64,130],"an":[65,177],"solution":[67],"applied":[73],"prediction.":[76],"Our":[77],"main":[78],"contributions":[79],"are:":[80],"(a)":[81],"identification":[83],"forms":[86],"exploit":[88],"parallelism":[89,146,161],"algorithm;":[94],"(b)":[95],"that":[99,162,182],"achieve":[100],"speedups":[101],"up":[102],"52.62":[104],"90.86,":[106],"respectively,":[107],"when":[108],"compared":[109],"a":[111,127,144,172],"sequential":[112],"implementation.":[113],"The":[114],"scales":[117],"with":[118,153],"input":[119],"data":[120,132,151],"size,":[121],"outperforming":[122],"related":[123],"work":[124],"results;":[125],"(c)":[126],"particular":[128],"organization":[129],"structures":[133],"order":[138],"optimize":[140],"their":[141],"efficiency;":[142],"(d)":[143],"potential":[145],"analysis":[147],"set":[152],"goal":[155],"measuring":[157],"amount":[159],"would":[163],"fact":[165],"be":[166,169],"available":[167],"exploited":[170],"by":[171],"implementation;":[174],"(e)":[176],"accurate":[178],"estimation":[180],"model":[181],"enabled":[183],"estimating":[184],"performance,":[187],"before":[188],"implementing":[189],"them.":[190]},"counts_by_year":[],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}
