{"id":"https://openalex.org/W2966840971","doi":"https://doi.org/10.1002/cpe.5468","title":"Using GPU to accelerate the pairwise structural RNA alignment with base pair probabilities","display_name":"Using GPU to accelerate the pairwise structural RNA alignment with base pair probabilities","publication_year":2019,"publication_date":"2019-08-01","ids":{"openalex":"https://openalex.org/W2966840971","doi":"https://doi.org/10.1002/cpe.5468","mag":"2966840971"},"language":"en","primary_location":{"id":"doi:10.1002/cpe.5468","is_oa":false,"landing_page_url":"https://doi.org/10.1002/cpe.5468","pdf_url":null,"source":{"id":"https://openalex.org/S11065456","display_name":"Concurrency and Computation Practice and Experience","issn_l":"1532-0626","issn":["1532-0626","1532-0634"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Concurrency and Computation: Practice and Experience","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/A5025518020","display_name":"D. Sundfeld","orcid":"https://orcid.org/0000-0002-5147-3698"},"institutions":[{"id":"https://openalex.org/I3129743071","display_name":"Instituto Federal de Educa\u00e7\u00e3o, Ci\u00eancia e Tecnologia de Bras\u00edlia","ror":"https://ror.org/03bk74w21","country_code":"BR","type":"education","lineage":["https://openalex.org/I1293487690","https://openalex.org/I2801200668","https://openalex.org/I3129743071"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Daniel Sundfeld","raw_affiliation_strings":["Information and Communication Technology Bras\u00edlia Federal Institute  Bras\u00edlia Brazil"],"raw_orcid":"https://orcid.org/0000-0002-5147-3698","affiliations":[{"raw_affiliation_string":"Information and Communication Technology Bras\u00edlia Federal Institute  Bras\u00edlia Brazil","institution_ids":["https://openalex.org/I3129743071"]}]},{"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/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":"George Teodoro","raw_affiliation_strings":["Department of Computer Science University of Bras\u00edlia  Bras\u00edlia Brazil"],"raw_orcid":"https://orcid.org/0000-0001-6289-3914","affiliations":[{"raw_affiliation_string":"Department of Computer Science University of Bras\u00edlia  Bras\u00edlia Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019722014","display_name":"Jakob H. Havgaard","orcid":"https://orcid.org/0000-0002-4816-814X"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I83467386","display_name":"IT University of Copenhagen","ror":"https://ror.org/02309jg23","country_code":"DK","type":"education","lineage":["https://openalex.org/I83467386"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Jakob H. Havgaard","raw_affiliation_strings":["Center for Non\u2010Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences University of Copenhagen  Copenhagen Denmark","Center for Non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Non\u2010Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences University of Copenhagen  Copenhagen Denmark","institution_ids":["https://openalex.org/I83467386"]},{"raw_affiliation_string":"Center for Non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004614832","display_name":"Jan Gorodkin","orcid":"https://orcid.org/0000-0001-5823-4000"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I83467386","display_name":"IT University of Copenhagen","ror":"https://ror.org/02309jg23","country_code":"DK","type":"education","lineage":["https://openalex.org/I83467386"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Jan Gorodkin","raw_affiliation_strings":["Center for Non\u2010Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences University of Copenhagen  Copenhagen Denmark","Center for Non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark"],"raw_orcid":"https://orcid.org/0000-0001-5823-4000","affiliations":[{"raw_affiliation_string":"Center for Non\u2010Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences University of Copenhagen  Copenhagen Denmark","institution_ids":["https://openalex.org/I83467386"]},{"raw_affiliation_string":"Center for Non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"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":["Department of Computer Science University of Bras\u00edlia  Bras\u00edlia Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science University of Bras\u00edlia  Bras\u00edlia Brazil","institution_ids":["https://openalex.org/I150729083"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5025518020"],"corresponding_institution_ids":["https://openalex.org/I3129743071"],"apc_list":{"value":4740,"currency":"USD","value_usd":4740},"apc_paid":null,"fwci":0.58,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.66080197,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"32","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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/T11482","display_name":"RNA modifications and cancer","score":0.9977999925613403,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9934999942779541,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.8717106580734253},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.7977790832519531},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.5897119641304016},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4851744771003723},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.390566885471344},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.33132296800613403},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3275214731693268},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22399544715881348},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08768865466117859}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8717106580734253},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7977790832519531},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.5897119641304016},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4851744771003723},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.390566885471344},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.33132296800613403},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3275214731693268},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22399544715881348},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08768865466117859},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1002/cpe.5468","is_oa":false,"landing_page_url":"https://doi.org/10.1002/cpe.5468","pdf_url":null,"source":{"id":"https://openalex.org/S11065456","display_name":"Concurrency and Computation Practice and Experience","issn_l":"1532-0626","issn":["1532-0626","1532-0634"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Concurrency and Computation: Practice and Experience","raw_type":"journal-article"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/b7b27b71-97af-4268-b9e8-6a45d0c0aea4","is_oa":false,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/b7b27b71-97af-4268-b9e8-6a45d0c0aea4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Sundfeld , D , Teodoro , G , Havgaard , J H , Gorodkin , J & Melo , A C M A 2020 , ' Using GPU to accelerate the pairwise structural RNA alignment with base pair probabilities ' , Concurrency Computation , vol. 32 , no. 10 , e5468 . https://doi.org/10.1002/cpe.5468","raw_type":"article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310484","display_name":"Teknologi og Produktion, Det Frie Forskningsr\u00e5d","ror":"https://ror.org/03ge1nb22"},{"id":"https://openalex.org/F4320313796","display_name":"Innovationsfonden","ror":"https://ror.org/00daj4111"},{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320321999","display_name":"Lundbeckfonden","ror":"https://ror.org/03hz8wd80"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320322928","display_name":"Danmarks Frie Forskningsfond","ror":"https://ror.org/02sptwz63"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1976021976","https://openalex.org/W1984675364","https://openalex.org/W2025763720","https://openalex.org/W2042844155","https://openalex.org/W2054931730","https://openalex.org/W2086561953","https://openalex.org/W2095145214","https://openalex.org/W2108865780","https://openalex.org/W2109553965","https://openalex.org/W2111773652","https://openalex.org/W2114094654","https://openalex.org/W2137356209","https://openalex.org/W2137709353","https://openalex.org/W2147394603","https://openalex.org/W2166745309","https://openalex.org/W2170157200","https://openalex.org/W2268094462","https://openalex.org/W2344543892","https://openalex.org/W2466930524","https://openalex.org/W2481510159","https://openalex.org/W2492384598","https://openalex.org/W2609873635","https://openalex.org/W2621218774"],"related_works":["https://openalex.org/W2487162673","https://openalex.org/W2793211469","https://openalex.org/W2949152769","https://openalex.org/W4372354731","https://openalex.org/W2942366970","https://openalex.org/W2807634898","https://openalex.org/W1692008701","https://openalex.org/W2597588799","https://openalex.org/W4360593462","https://openalex.org/W2562400057"],"abstract_inverted_index":{"Summary":[0],"Structural":[1],"alignments":[2],"of":[3,58,74,196,202,206,227],"Ribonucleic":[4],"acid":[5],"(RNA)":[6],"sequences":[7,188],"solved":[8],"by":[9],"the":[10,50,64,75,79,84,123,133,136,141,144,149,155,162,169,174,203,207,212,230,237],"Sankoff":[11,76,208],"algorithm":[12],"are":[13,178],"computationally":[14],"expensive":[15],"and":[16,69,82,113,125,245,253],"often":[17],"require":[18],"constraints":[19],"to":[20,39,49,99,140,148,173,223,250],"be":[21],"used":[22],"in":[23,37,108,127,152,161,180],"practice.":[24],"Modern":[25],"Graphics":[26],"Processing":[27],"Units":[28],"(GPUs)":[29],"contain":[30],"more":[31],"than":[32],"1000":[33],"cores,":[34,218],"which":[35],"compute":[36],"parallel":[38],"speed":[40],"up":[41],"applications.":[42],"Here,":[43],"we":[44],"present":[45],"a":[46,95,128,198,225],"GPU\u2010based":[47],"solution":[48],"RNA":[51,187],"structural":[52],"alignment":[53],"problem":[54],"that":[55,146,171,190],"makes":[56],"use":[57],"precalculated":[59],"base":[60],"pair":[61],"probabilities":[62],"on":[63,122,216,229],"individual":[65],"sequences.":[66],"We":[67,118],"designed":[68],"developed":[70],"an":[71,166],"unconstrained":[72,204],"version":[73,193,201,205,214],"algorithm,":[77],"obtaining":[78],"optimal":[80],"result":[81],"calculating":[83,143],"entire":[85],"four\u2010dimension":[86],"dynamic":[87],"programming":[88],"matrix":[89,105,111],"(4D":[90],"DP).":[91],"Our":[92],"approach":[93,220],"uses":[94],"two\u2010level":[96,129],"wavefront":[97,120,137],"strategy":[98],"exploit":[100],"parallelism.":[101],"The":[102,182],"4D":[103],"DP":[104],"is":[106,138,164,194,221],"divided":[107],"one":[109],"external":[110],"(EM)":[112],"several":[114],"internal":[115],"matrices":[116],"(IM).":[117],"applied":[119,139],"strategies":[121],"EM":[124,163],"IMs":[126],"hierarchical":[130],"way.":[131],"At":[132],"first":[134],"level,":[135,157],"EM,":[142],"cells":[145,170],"belong":[147,172],"same":[150,175],"diagonal":[151,177],"parallel.":[153,181],"In":[154,234],"second":[156],"since":[158],"each":[159],"cell":[160],"itself":[165],"IM":[167,176],"matrix,":[168],"calculated":[179],"results":[183],"obtained":[184],"with":[185,211],"real":[186],"show":[189],"our":[191,219],"GPU":[192],"capable":[195],"outperforming":[197],"multicore":[199],"CPU":[200],"algorithm.":[209],"Compared":[210],"CPU\u2010based":[213],"running":[215],"32":[217],"able":[222],"achieve":[224],"speedup":[226],"7.81x":[228],"NVidia":[231],"Tesla":[232],"P100.":[233],"this":[235],"case,":[236],"execution":[238],"time":[239],"was":[240],"reduced":[241],"from":[242],"6":[243],"hours":[244],"18":[246],"minutes":[247,252],"(32":[248],"cores)":[249],"48":[251],"20":[254],"seconds":[255],"(GPU).":[256]},"counts_by_year":[{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}