{"id":"https://openalex.org/W2113995501","doi":"https://doi.org/10.1145/2016604.2016642","title":"Parametrizing multicore architectures for multiple sequence alignment","display_name":"Parametrizing multicore architectures for multiple sequence alignment","publication_year":2011,"publication_date":"2011-05-03","ids":{"openalex":"https://openalex.org/W2113995501","doi":"https://doi.org/10.1145/2016604.2016642","mag":"2113995501"},"language":"en","primary_location":{"id":"doi:10.1145/2016604.2016642","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2016604.2016642","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Computing Frontiers","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://zenodo.org/record/3438409","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041358312","display_name":"Sebasti\u00e1n Isaza","orcid":"https://orcid.org/0000-0003-4487-7624"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Sebastian Isaza","raw_affiliation_strings":["Delft University of Technology, The Netherlands","Delft University of Technology, The Netherlands;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Delft University of Technology, The Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Delft University of Technology, The Netherlands;","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102746770","display_name":"Friman S\u00e1nchez","orcid":"https://orcid.org/0000-0002-0949-7688"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Friman Sanchez","raw_affiliation_strings":["Technical University of Catalonia, Spain","Technical University of Catalonia (Spain)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Technical University of Catalonia, Spain","institution_ids":["https://openalex.org/I9617848"]},{"raw_affiliation_string":"Technical University of Catalonia (Spain)","institution_ids":["https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026623616","display_name":"Felipe Cabarcas","orcid":"https://orcid.org/0000-0002-8966-0405"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Felipe Cabarcas","raw_affiliation_strings":["Technical University of Catalonia and Barcelona Supercomputing Center, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Technical University of Catalonia and Barcelona Supercomputing Center, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082472991","display_name":"Alex Ram\u00edrez","orcid":"https://orcid.org/0000-0003-3317-4616"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Alex Ramirez","raw_affiliation_strings":["Technical University of Catalonia and Barcelona Supercomputing Center, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Technical University of Catalonia and Barcelona Supercomputing Center, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075050234","display_name":"Georgi Gaydadjiev","orcid":"https://orcid.org/0000-0002-3678-7007"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Georgi Gaydadjiev","raw_affiliation_strings":["Delft University of Technology, The Netherlands","Delft University of Technology, The Netherlands;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Delft University of Technology, The Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Delft University of Technology, The Netherlands;","institution_ids":["https://openalex.org/I98358874"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1331,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.54056283,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9915000200271606,"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":0.9878000020980835,"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":0.8888043165206909},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7141921520233154},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.7018637657165527},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.64858478307724},{"id":"https://openalex.org/keywords/memory-bandwidth","display_name":"Memory bandwidth","score":0.5243000388145447},{"id":"https://openalex.org/keywords/latency","display_name":"Latency (audio)","score":0.4737088084220886},{"id":"https://openalex.org/keywords/bandwidth","display_name":"Bandwidth (computing)","score":0.45703306794166565},{"id":"https://openalex.org/keywords/cache","display_name":"Cache","score":0.4564918875694275},{"id":"https://openalex.org/keywords/synchronization","display_name":"Synchronization (alternating current)","score":0.41939690709114075},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.4055114984512329},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3825565278530121},{"id":"https://openalex.org/keywords/channel","display_name":"Channel (broadcasting)","score":0.09826594591140747}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8888043165206909},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7141921520233154},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.7018637657165527},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.64858478307724},{"id":"https://openalex.org/C188045654","wikidata":"https://www.wikidata.org/wiki/Q17148339","display_name":"Memory bandwidth","level":2,"score":0.5243000388145447},{"id":"https://openalex.org/C82876162","wikidata":"https://www.wikidata.org/wiki/Q17096504","display_name":"Latency (audio)","level":2,"score":0.4737088084220886},{"id":"https://openalex.org/C2776257435","wikidata":"https://www.wikidata.org/wiki/Q1576430","display_name":"Bandwidth (computing)","level":2,"score":0.45703306794166565},{"id":"https://openalex.org/C115537543","wikidata":"https://www.wikidata.org/wiki/Q165596","display_name":"Cache","level":2,"score":0.4564918875694275},{"id":"https://openalex.org/C2778562939","wikidata":"https://www.wikidata.org/wiki/Q1298791","display_name":"Synchronization (alternating current)","level":3,"score":0.41939690709114075},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.4055114984512329},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3825565278530121},{"id":"https://openalex.org/C127162648","wikidata":"https://www.wikidata.org/wiki/Q16858953","display_name":"Channel (broadcasting)","level":2,"score":0.09826594591140747},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2016604.2016642","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2016604.2016642","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Computing Frontiers","raw_type":"proceedings-article"},{"id":"pmh:oai:zenodo.org:3438409","is_oa":true,"landing_page_url":"https://zenodo.org/record/3438409","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferencePaper"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:3438409","is_oa":true,"landing_page_url":"https://zenodo.org/record/3438409","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferencePaper"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.4099999964237213,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G6812521406","display_name":null,"funder_award_id":"SARC 27648ENCORE 249059","funder_id":"https://openalex.org/F4320334960","funder_display_name":"Seventh Framework Programme"}],"funders":[{"id":"https://openalex.org/F4320323868","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96"},{"id":"https://openalex.org/F4320334960","display_name":"Seventh Framework Programme","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320338388","display_name":"Eurostars","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1504133853","https://openalex.org/W1515512963","https://openalex.org/W1519266993","https://openalex.org/W1975975525","https://openalex.org/W2013420473","https://openalex.org/W2052924095","https://openalex.org/W2059807497","https://openalex.org/W2077163732","https://openalex.org/W2087064593","https://openalex.org/W2089499735","https://openalex.org/W2103844840","https://openalex.org/W2106882534","https://openalex.org/W2144316495","https://openalex.org/W2146379626","https://openalex.org/W2150871235","https://openalex.org/W2155518645","https://openalex.org/W2157909358","https://openalex.org/W2164856315","https://openalex.org/W2165949232","https://openalex.org/W2184753910"],"related_works":["https://openalex.org/W2128523353","https://openalex.org/W2152099439","https://openalex.org/W1984163603","https://openalex.org/W2291648581","https://openalex.org/W3130422087","https://openalex.org/W2107644726","https://openalex.org/W2406856881","https://openalex.org/W2011868109","https://openalex.org/W2031026393","https://openalex.org/W2063611263"],"abstract_inverted_index":{"Sequence":[0,133],"alignment":[1],"is":[2,123,168,173],"one":[3,125],"of":[4,15,22,38,52,57,67,89,92,100,126,161,190,219,235],"the":[5,12,19,23,36,40,58,61,86,98,104,117,127,154,159,191,201,209],"fundamental":[6],"tasks":[7,210],"in":[8,44,163],"bioinformatics.":[9],"Due":[10],"to":[11,153,175,214],"exponential":[13],"growth":[14],"biological":[16],"data":[17,137,162],"and":[18,60,79,102,115,141,158,194],"computational":[20],"complexity":[21],"algorithms":[24],"used,":[25],"high":[26,155],"performance":[27,69,87,118,234],"computing":[28],"systems":[29,49],"are":[30,139],"required.":[31],"Although":[32],"multicore":[33,95,111],"architectures":[34],"have":[35],"potential":[37],"exploiting":[39],"task-level":[41],"parallelism":[42],"found":[43],"these":[45],"workloads,":[46],"efficiently":[47],"harnessing":[48],"with":[50,97,184],"hundreds":[51],"cores":[53,237],"requires":[54],"deep":[55],"understanding":[56],"applications":[59],"architecture.":[62],"When":[63],"incorporating":[64],"large":[65,164,217],"numbers":[66],"cores,":[68],"scalability":[70],"will":[71],"likely":[72],"saturate":[73],"shared":[74],"hardware":[75,206],"resources":[76],"like":[77],"buses":[78],"memories.":[80],"In":[81],"this":[82],"paper":[83],"we":[84,107,142,222,231],"evaluate":[85],"impact":[88],"various":[90],"configurations":[91],"an":[93],"accelerator-based":[94],"architecture":[96],"aim":[99],"revealing":[101],"quantifying":[103],"bottlenecks.":[105],"Then,":[106],"compare":[108],"against":[109],"a":[110,180,205,216,226],"using":[112,204,225],"general-purpose":[113,236],"processors":[114],"discuss":[116],"gap.":[119],"Our":[120],"target":[121],"application":[122],"ClustalW,":[124],"most":[128,189],"popular":[129],"programs":[130],"for":[131,208],"Multiple":[132],"Alignment.":[134],"Different":[135],"input":[136],"sets":[138],"characterized":[140],"show":[143,150,223],"how":[144],"they":[145],"influence":[146],"performance.":[147,178],"Simulation":[148],"results":[149],"that":[151,224],"due":[152],"computation-to-communication":[156],"ratio":[157],"transfer":[160],"chunks,":[165],"memory":[166,192],"latency":[167],"well":[169],"tolerated.":[170],"However,":[171],"bandwidth":[172],"critical":[174],"achieving":[176],"maximum":[177],"Using":[179],"32KB":[181],"cache":[182],"configuration":[183],"4":[185],"banks":[186],"can":[187,232],"capture":[188],"traffic":[193],"therefore":[195],"avoid":[196],"expensive":[197],"off-chip":[198],"transactions.":[199],"On":[200],"other":[202],"hand,":[203],"queue":[207],"synchronization":[211],"allows":[212],"us":[213],"handle":[215],"number":[218],"cores.":[220],"Finally,":[221],"simple":[227],"load":[228],"balancing":[229],"strategy,":[230],"increase":[233],"by":[238],"28%.":[239]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
