{"id":"https://openalex.org/W2342894425","doi":"https://doi.org/10.1109/tcbb.2015.2495149","title":"BowMapCL: Burrows-Wheeler Mapping on Multiple Heterogeneous Accelerators","display_name":"BowMapCL: Burrows-Wheeler Mapping on Multiple Heterogeneous Accelerators","publication_year":2015,"publication_date":"2015-10-26","ids":{"openalex":"https://openalex.org/W2342894425","doi":"https://doi.org/10.1109/tcbb.2015.2495149","mag":"2342894425","pmid":"https://pubmed.ncbi.nlm.nih.gov/26529775"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2015.2495149","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2495149","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5031803511","display_name":"David De Sa Nogueira","orcid":"https://orcid.org/0000-0002-2173-7154"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"David Nogueira","raw_affiliation_strings":["INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal","INESC-ID / Instituto Superior T\u00e9cnico -- Universidade de Lisboa, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]},{"raw_affiliation_string":"INESC-ID / Instituto Superior T\u00e9cnico -- Universidade de Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075054918","display_name":"Pedro Tom\u00e1s","orcid":"https://orcid.org/0000-0001-8083-4432"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Pedro Tomas","raw_affiliation_strings":["INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal","INESC-ID / Instituto Superior T\u00e9cnico -- Universidade de Lisboa, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]},{"raw_affiliation_string":"INESC-ID / Instituto Superior T\u00e9cnico -- Universidade de Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015710714","display_name":"Nuno Roma","orcid":"https://orcid.org/0000-0003-2491-4977"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Nuno Roma","raw_affiliation_strings":["INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal","INESC-ID / Instituto Superior T\u00e9cnico -- Universidade de Lisboa, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]},{"raw_affiliation_string":"INESC-ID / Instituto Superior T\u00e9cnico -- Universidade de Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.5264,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.83037504,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"13","issue":"5","first_page":"926","last_page":"938"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9994000196456909,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9994000196456909,"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/T12072","display_name":"Machine Learning and Algorithms","score":0.9613999724388123,"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9381999969482422,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43511682748794556}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43511682748794556}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2015.2495149","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2495149","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26529775","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26529775","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4206994534","display_name":null,"funder_award_id":"PTDC/EEA-ELC/117329/2010","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G8288186299","display_name":null,"funder_award_id":"PTDC/EEA-ELC/117329/2010","funder_id":"https://openalex.org/F4320337197","funder_display_name":"Nuclear Fuel Cycle and Supply Chain"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320337197","display_name":"Nuclear Fuel Cycle and Supply Chain","ror":"https://ror.org/05tj7dm33"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1514735749","https://openalex.org/W1530458829","https://openalex.org/W1976682045","https://openalex.org/W1976978590","https://openalex.org/W1985108724","https://openalex.org/W2002638840","https://openalex.org/W2015831381","https://openalex.org/W2031445984","https://openalex.org/W2037748100","https://openalex.org/W2063099138","https://openalex.org/W2065461987","https://openalex.org/W2068996722","https://openalex.org/W2097341408","https://openalex.org/W2103441770","https://openalex.org/W2107824361","https://openalex.org/W2112113834","https://openalex.org/W2115036455","https://openalex.org/W2117683095","https://openalex.org/W2124985265","https://openalex.org/W2134283755","https://openalex.org/W2158322625","https://openalex.org/W2158714788","https://openalex.org/W2158874082","https://openalex.org/W2161488606","https://openalex.org/W2168334921","https://openalex.org/W2178915921","https://openalex.org/W2533248932","https://openalex.org/W6630466623","https://openalex.org/W6683504902"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"The":[0],"computational":[1],"demand":[2],"of":[3,10,19,30,79,191],"exact-search":[4,50],"procedures":[5],"has":[6],"pressed":[7],"the":[8,16,31,56,77,128,163,184,192,196],"exploitation":[9,78],"parallel":[11],"processing":[12,194],"accelerators":[13],"to":[14,39,64,92,102,141,158],"reduce":[15],"execution":[17],"time":[18],"many":[20],"applications.":[21],"However,":[22],"this":[23,46],"often":[24],"imposes":[25],"strict":[26],"restrictions":[27],"in":[28,195],"terms":[29],"problem":[32],"size":[33],"and":[34,59,81,88,106,113,121,154,156,171,175],"implementation":[35,73],"efforts,":[36],"mainly":[37],"due":[38],"their":[40],"possibly":[41,82],"distinct":[42,177,198],"architectures.":[43],"To":[44],"circumvent":[45],"limitation,":[47],"a":[48,71,135,188],"new":[49],"alignment":[51],"tool":[52],"(BowMapCL)":[53],"based":[54,69],"on":[55,70],"Burrows-Wheeler":[57],"Transform":[58],"FM-Index":[60],"is":[61,68,138],"presented.":[62],"Contrasting":[63],"other":[65],"alternatives,":[66],"BowMapCL":[67,98,133,181],"unified":[72],"using":[74],"OpenCL,":[75],"allowing":[76],"multiple":[80,109,174],"different":[83],"devices":[84,178],"(e.g.,":[85],"NVIDIA,":[86],"AMD/ATI,":[87],"Intel":[89],"GPUs/APUs).":[90],"Furthermore,":[91],"efficiently":[93,182],"exploit":[94],"such":[95],"heterogeneous":[96],"architectures,":[97],"incorporates":[99],"several":[100,197],"techniques":[101],"promote":[103],"its":[104],"performance":[105],"scalability,":[107],"including":[108],"buffering,":[110],"work-queue":[111],"task-distribution,":[112],"dynamic":[114],"load-balancing,":[115],"together":[116],"with":[117,125],"index":[118],"partitioning,":[119],"bit-encoding,":[120],"sampling.":[122],"When":[123,173],"compared":[124],"state-of-the-art":[126,166],"tools,":[127],"attained":[129],"results":[130],"showed":[131],"that":[132],"(using":[134],"single":[136],"GPU)":[137],"2":[139],"\u00d7":[140,143,160],"7.5":[142],"faster":[144,161],"than":[145,162],"mainstream":[146],"multi-threaded":[147],"CPU":[148],"BWT-based":[149],"aligners,":[150],"like":[151],"Bowtie,":[152],"BWA,":[153],"SOAP2;":[155],"up":[157],"4":[159],"best":[164],"performing":[165],"GPU":[167],"implementations":[168],"(namely,":[169],"SOAP3":[170],"HPG-BWT).":[172],"completely":[176],"are":[179],"considered,":[180],"scales":[183],"offered":[185],"throughput,":[186],"ensuring":[187],"convenient":[189],"load-balance":[190],"involved":[193],"devices.":[199]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}