{"id":"https://openalex.org/W1996717081","doi":"https://doi.org/10.1109/tcbb.2014.2377716","title":"Boosting the FM-Index on the GPU: Effective Techniques to Mitigate Random Memory Access","display_name":"Boosting the FM-Index on the GPU: Effective Techniques to Mitigate Random Memory Access","publication_year":2014,"publication_date":"2014-12-04","ids":{"openalex":"https://openalex.org/W1996717081","doi":"https://doi.org/10.1109/tcbb.2014.2377716","mag":"1996717081","pmid":"https://pubmed.ncbi.nlm.nih.gov/26451818"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2014.2377716","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2377716","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/7293246/06975110.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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":true,"oa_status":"bronze","oa_url":"https://ieeexplore.ieee.org/ielx7/8857/7293246/06975110.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072699100","display_name":"Alejandro Chac\u00f3n","orcid":"https://orcid.org/0000-0001-8851-7618"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Alejandro Chacon","raw_affiliation_strings":["Computer Architecture and Operating Systems, Universitat Aut\u00f2noma de Barcelona, Bellaterra, Spain"],"raw_orcid":"https://orcid.org/0000-0001-8851-7618","affiliations":[{"raw_affiliation_string":"Computer Architecture and Operating Systems, Universitat Aut\u00f2noma de Barcelona, Bellaterra, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052502603","display_name":"Santiago Marco\u2010Sola","orcid":"https://orcid.org/0000-0001-7951-3914"},"institutions":[{"id":"https://openalex.org/I4210142206","display_name":"Centro Nacional de An\u00e1lisis Gen\u00f3mico","ror":"https://ror.org/03mynna02","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210142206"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Santiago Marco-Sola","raw_affiliation_strings":["Centro Nacional de An\u00e1lisis Gen\u00f3mico, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Nacional de An\u00e1lisis Gen\u00f3mico, Barcelona, Spain","institution_ids":["https://openalex.org/I4210142206"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031177539","display_name":"Antonio Espinosa","orcid":"https://orcid.org/0000-0002-6460-3789"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Antonio Espinosa","raw_affiliation_strings":["Computer Architecture and Operating Systems, Universitat Aut\u00f2noma de Barcelona, Bellaterra, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Architecture and Operating Systems, Universitat Aut\u00f2noma de Barcelona, Bellaterra, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031469755","display_name":"Paolo Ribeca","orcid":"https://orcid.org/0000-0001-5599-3933"},"institutions":[{"id":"https://openalex.org/I1287548271","display_name":"The Pirbright Institute","ror":"https://ror.org/04xv01a59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1287548271","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I4210142206","display_name":"Centro Nacional de An\u00e1lisis Gen\u00f3mico","ror":"https://ror.org/03mynna02","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210142206"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"Paolo Ribeca","raw_affiliation_strings":["Centro Nacional de An\u00e1lisis Gen\u00f3mico, Barcelona, Spain","Pirbright Institute, Woking GU24 0NF, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Nacional de An\u00e1lisis Gen\u00f3mico, Barcelona, Spain","institution_ids":["https://openalex.org/I4210142206"]},{"raw_affiliation_string":"Pirbright Institute, Woking GU24 0NF, United Kingdom","institution_ids":["https://openalex.org/I1287548271"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051140834","display_name":"Juan Carlos Moure","orcid":"https://orcid.org/0000-0001-6697-0331"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Juan Carlos Moure","raw_affiliation_strings":["Computer Architecture and Operating Systems, Universitat Aut\u00f2noma de Barcelona, Bellaterra, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Architecture and Operating Systems, Universitat Aut\u00f2noma de Barcelona, Bellaterra, Spain","institution_ids":["https://openalex.org/I123044942"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5072699100"],"corresponding_institution_ids":["https://openalex.org/I123044942"],"apc_list":null,"apc_paid":null,"fwci":1.6914,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.87217492,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"12","issue":"5","first_page":"1048","last_page":"1059"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9995999932289124,"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":0.9995999932289124,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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/T12029","display_name":"DNA and Biological Computing","score":0.9832000136375427,"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":0.859623908996582},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.7516825199127197},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.712177038192749},{"id":"https://openalex.org/keywords/random-access","display_name":"Random access","score":0.5692129731178284},{"id":"https://openalex.org/keywords/boosting","display_name":"Boosting (machine learning)","score":0.48009756207466125},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.46017661690711975},{"id":"https://openalex.org/keywords/out-of-core-algorithm","display_name":"Out-of-core algorithm","score":0.44496089220046997},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.4353589713573456},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.4215862452983856},{"id":"https://openalex.org/keywords/high-memory","display_name":"High memory","score":0.4109462797641754},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.26319730281829834},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.185007244348526},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.174478679895401},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1430054008960724},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.08497786521911621}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.859623908996582},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.7516825199127197},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.712177038192749},{"id":"https://openalex.org/C101722063","wikidata":"https://www.wikidata.org/wiki/Q218825","display_name":"Random access","level":2,"score":0.5692129731178284},{"id":"https://openalex.org/C46686674","wikidata":"https://www.wikidata.org/wiki/Q466303","display_name":"Boosting (machine learning)","level":2,"score":0.48009756207466125},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.46017661690711975},{"id":"https://openalex.org/C79470037","wikidata":"https://www.wikidata.org/wiki/Q279748","display_name":"Out-of-core algorithm","level":2,"score":0.44496089220046997},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.4353589713573456},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.4215862452983856},{"id":"https://openalex.org/C2781357197","wikidata":"https://www.wikidata.org/wiki/Q5757597","display_name":"High memory","level":2,"score":0.4109462797641754},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.26319730281829834},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.185007244348526},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.174478679895401},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1430054008960724},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.08497786521911621}],"mesh":[{"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":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D004867","descriptor_name":"Equipment Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004867","descriptor_name":"Equipment Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004867","descriptor_name":"Equipment Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":"Q000295","qualifier_name":"instrumentation","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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016248","descriptor_name":"Computer Storage Devices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016248","descriptor_name":"Computer Storage Devices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016248","descriptor_name":"Computer Storage Devices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019544","descriptor_name":"Equipment Failure Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019544","descriptor_name":"Equipment Failure Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019544","descriptor_name":"Equipment Failure Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2014.2377716","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2377716","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/7293246/06975110.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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:26451818","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26451818","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},{"id":"pmh:oai:ddd.uab.cat:131873","is_oa":true,"landing_page_url":"https://ddd.uab.cat/record/131873","pdf_url":"https://ddd.uab.cat/record/131873","source":{"id":"https://openalex.org/S4306400380","display_name":"Dip\u00f2sit Digital de Documents de la UAB (Universitat Aut\u00f2noma de Barcelona)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123044942","host_organization_name":"Universitat Aut\u00f2noma de Barcelona","host_organization_lineage":["https://openalex.org/I123044942"],"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":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1109/tcbb.2014.2377716","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2377716","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/7293246/06975110.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1328468445","display_name":null,"funder_award_id":"TIN2011-28689","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G3430886672","display_name":null,"funder_award_id":"TIN2011-28689-C02-01","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G4465271416","display_name":null,"funder_award_id":"BBS/E/I/00001942","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1996717081.pdf","grobid_xml":"https://content.openalex.org/works/W1996717081.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W26356079","https://openalex.org/W1545099940","https://openalex.org/W1982088757","https://openalex.org/W1984656893","https://openalex.org/W1984897969","https://openalex.org/W2011218124","https://openalex.org/W2015831381","https://openalex.org/W2025648894","https://openalex.org/W2034798008","https://openalex.org/W2037748100","https://openalex.org/W2068996722","https://openalex.org/W2091519884","https://openalex.org/W2103441770","https://openalex.org/W2107824361","https://openalex.org/W2110195531","https://openalex.org/W2124985265","https://openalex.org/W2141978199","https://openalex.org/W2145186114","https://openalex.org/W2149766518","https://openalex.org/W2151224499","https://openalex.org/W2158322625","https://openalex.org/W2161488606","https://openalex.org/W2178915921","https://openalex.org/W2269349250","https://openalex.org/W6693413133"],"related_works":["https://openalex.org/W3062287","https://openalex.org/W2380390332","https://openalex.org/W2742145873","https://openalex.org/W4245975140","https://openalex.org/W2062253548","https://openalex.org/W4225414539","https://openalex.org/W4289522463","https://openalex.org/W1977763331","https://openalex.org/W4318483369","https://openalex.org/W2678153835"],"abstract_inverted_index":{"The":[0,126],"recent":[1],"advent":[2],"of":[3,10,23,67,123,128,144],"high-throughput":[4],"sequencing":[5],"machines":[6],"producing":[7],"big":[8],"amounts":[9],"short":[11],"reads":[12],"has":[13],"boosted":[14],"the":[15,38,64,89,93,121,172,176,180],"interest":[16],"in":[17,46,85],"efficient":[18],"string":[19],"searching":[20],"techniques.":[21],"As":[22],"today,":[24],"many":[25],"mainstream":[26],"sequence":[27],"alignment":[28],"software":[29],"tools":[30],"rely":[31],"on":[32,72,92,107,148,175],"a":[33,55,112,158],"special":[34],"data":[35],"structure,":[36],"called":[37],"FM-index,":[39],"which":[40],"allows":[41],"for":[42],"fast":[43],"exact":[44],"searches":[45,52],"large":[47],"genomic":[48],"references.":[49],"However,":[50],"such":[51],"translate":[53],"into":[54],"pseudo-random":[56],"memory":[57,62,90,109,124],"access":[58,63],"pattern,":[59],"thus":[60],"making":[61],"limiting":[65],"factor":[66],"all":[68],"computation-efficient":[69],"implementations,":[70],"both":[71],"CPUs":[73],"and":[74,111,130,163],"GPUs.":[75],"Here,":[76],"we":[77],"show":[78],"that":[79,136],"several":[80],"strategies":[81],"can":[82,98,115],"be":[83,99,116],"put":[84],"place":[86],"to":[87,118,139,167],"remove":[88],"bottleneck":[91],"GPU:":[94],"more":[95,103],"compact":[96],"indexes":[97],"implemented":[100],"by":[101,179],"having":[102],"threads":[104],"work":[105],"cooperatively":[106],"larger":[108],"blocks,":[110],"k-step":[113],"FM-index":[114,173],"used":[117],"further":[119],"reduce":[120],"number":[122],"accesses.":[125],"combination":[127],"those":[129],"other":[131],"optimisations":[132],"yields":[133],"an":[134],"implementation":[135,174],"is":[137],"able":[138],"process":[140],"about":[141,153,164],"two":[142],"Gbases":[143],"queries":[145],"per":[146],"second":[147],"our":[149],"test":[150],"platform,":[151],"being":[152],"8":[154],"\u00d7":[155,166,169],"faster":[156,170],"than":[157,171],"comparable":[159],"multi-core":[160],"CPU":[161],"version,":[162],"3":[165],"5":[168],"GPU":[177],"provided":[178],"recently":[181],"announced":[182],"Nvidia":[183],"NVBIO":[184],"bioinformatics":[185],"library.":[186]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
