{"id":"https://openalex.org/W3033334618","doi":"https://doi.org/10.1109/tcbb.2020.3000253","title":"Compressed Sparse FM-Index: Fast Sequence Alignment Using Large K-Steps","display_name":"Compressed Sparse FM-Index: Fast Sequence Alignment Using Large K-Steps","publication_year":2020,"publication_date":"2020-06-05","ids":{"openalex":"https://openalex.org/W3033334618","doi":"https://doi.org/10.1109/tcbb.2020.3000253","mag":"3033334618","pmid":"https://pubmed.ncbi.nlm.nih.gov/32750858"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2020.3000253","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3000253","pdf_url":null,"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":"green","oa_url":"https://upcommons.upc.edu/bitstreams/afe5d971-3573-4150-80e9-4c44df8c5d7d/download","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072178927","display_name":"Rub\u00e9n Langarita","orcid":"https://orcid.org/0000-0002-6080-724X"},"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":true,"raw_author_name":"Ruben Langarita","raw_affiliation_strings":["Barcelona Supercomputing Center, Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0002-6080-724X","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049697257","display_name":"Adri\u00e0 Armejach","orcid":"https://orcid.org/0000-0003-2869-668X"},"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":"Adria Armejach","raw_affiliation_strings":["Barcelona Supercomputing Center, Barcelona, Spain","Universitat Polit\u00e8cnica de Catalunya, Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0003-2869-668X","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"Universitat Polit\u00e8cnica de Catalunya, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047597929","display_name":"Javier Setoa\u00edn","orcid":"https://orcid.org/0000-0002-9701-2352"},"institutions":[{"id":"https://openalex.org/I2801109035","display_name":"ARM (United Kingdom)","ror":"https://ror.org/04mmhzs81","country_code":"GB","type":"company","lineage":["https://openalex.org/I2801109035"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Javier Setoain","raw_affiliation_strings":["Arm, Cambridge, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-9701-2352","affiliations":[{"raw_affiliation_string":"Arm, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I2801109035"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028406181","display_name":"Pablo Ib\u00e1\u00f1ez","orcid":"https://orcid.org/0000-0002-5916-7898"},"institutions":[{"id":"https://openalex.org/I255234318","display_name":"Universidad de Zaragoza","ror":"https://ror.org/012a91z28","country_code":"ES","type":"education","lineage":["https://openalex.org/I255234318"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Pablo Ibanez-Marin","raw_affiliation_strings":["Departamento de Inform\u00e1tica e Ingenier\u00eda de Sistemas, Universidad de Zaragoza, Mar\u00eda de Luna 1, Zaragoza, Spain"],"raw_orcid":"https://orcid.org/0000-0002-5916-7898","affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica e Ingenier\u00eda de Sistemas, Universidad de Zaragoza, Mar\u00eda de Luna 1, Zaragoza, Spain","institution_ids":["https://openalex.org/I255234318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073821260","display_name":"Jes\u00fas Alastruey-Bened\u00e9","orcid":"https://orcid.org/0000-0003-4164-5078"},"institutions":[{"id":"https://openalex.org/I255234318","display_name":"Universidad de Zaragoza","ror":"https://ror.org/012a91z28","country_code":"ES","type":"education","lineage":["https://openalex.org/I255234318"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jesus Alastruey-Benede","raw_affiliation_strings":["Departamento de Inform\u00e1tica e Ingenier\u00eda de Sistemas, Universidad de Zaragoza, Mar\u00eda de Luna 1, Zaragoza, Spain"],"raw_orcid":"https://orcid.org/0000-0003-4164-5078","affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica e Ingenier\u00eda de Sistemas, Universidad de Zaragoza, Mar\u00eda de Luna 1, Zaragoza, Spain","institution_ids":["https://openalex.org/I255234318"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088729105","display_name":"Miquel Moret\u00f3","orcid":"https://orcid.org/0000-0002-9848-8758"},"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":"Miquel Moreto","raw_affiliation_strings":["Barcelona Supercomputing Center, Barcelona, Spain","Universitat Polit\u00e8cnica de Catalunya, Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0002-9848-8758","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"Universitat Polit\u00e8cnica de Catalunya, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5072178927"],"corresponding_institution_ids":["https://openalex.org/I2799803557","https://openalex.org/I9617848"],"apc_list":null,"apc_paid":null,"fwci":0.816,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.78848564,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"19","issue":"1","first_page":"355","last_page":"368"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9994000196456909,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9763000011444092,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.730776309967041},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.5712922811508179},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4730369746685028},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.4568191170692444},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.4481012523174286},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4294244647026062},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3901381492614746},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.22768676280975342},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.10593727231025696},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.0922069251537323}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.730776309967041},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.5712922811508179},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4730369746685028},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.4568191170692444},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.4481012523174286},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4294244647026062},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3901381492614746},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.22768676280975342},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.10593727231025696},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0922069251537323},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2020.3000253","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3000253","pdf_url":null,"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:32750858","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32750858","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:upcommons.upc.edu:2117/337048","is_oa":true,"landing_page_url":"https://hdl.handle.net/2117/337048","pdf_url":"https://upcommons.upc.edu/bitstreams/afe5d971-3573-4150-80e9-4c44df8c5d7d/download","source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"pmh:oai:upcommons.upc.edu:2117/337048","is_oa":true,"landing_page_url":"https://hdl.handle.net/2117/337048","pdf_url":"https://upcommons.upc.edu/bitstreams/afe5d971-3573-4150-80e9-4c44df8c5d7d/download","source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.5299999713897705}],"awards":[{"id":"https://openalex.org/G6456004180","display_name":null,"funder_award_id":"2017-SGR-1414","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G6712513641","display_name":null,"funder_award_id":"2017-SGR-1328","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"}],"funders":[{"id":"https://openalex.org/F4320321505","display_name":"Generalitat de Catalunya","ror":"https://ror.org/01bg62x04"},{"id":"https://openalex.org/F4320326208","display_name":"Gobierno de Arag\u00f3n","ror":"https://ror.org/0425pg203"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3033334618.pdf","grobid_xml":"https://content.openalex.org/works/W3033334618.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W794840634","https://openalex.org/W1828154403","https://openalex.org/W1904861952","https://openalex.org/W1962019683","https://openalex.org/W1982088757","https://openalex.org/W1996717081","https://openalex.org/W2002555321","https://openalex.org/W2011175593","https://openalex.org/W2015831381","https://openalex.org/W2037113830","https://openalex.org/W2037748100","https://openalex.org/W2055043387","https://openalex.org/W2068448872","https://openalex.org/W2068996722","https://openalex.org/W2070102345","https://openalex.org/W2087064593","https://openalex.org/W2091519884","https://openalex.org/W2097341408","https://openalex.org/W2102278945","https://openalex.org/W2103441770","https://openalex.org/W2116730320","https://openalex.org/W2124985265","https://openalex.org/W2128591967","https://openalex.org/W2132967231","https://openalex.org/W2133098231","https://openalex.org/W2134696992","https://openalex.org/W2135326109","https://openalex.org/W2138270253","https://openalex.org/W2143124024","https://openalex.org/W2145186114","https://openalex.org/W2146379626","https://openalex.org/W2146496959","https://openalex.org/W2149766518","https://openalex.org/W2158322625","https://openalex.org/W2158714788","https://openalex.org/W2158874082","https://openalex.org/W2161488606","https://openalex.org/W2220328383","https://openalex.org/W2222086580","https://openalex.org/W2340076492","https://openalex.org/W2560228154","https://openalex.org/W2756866639","https://openalex.org/W2789784730","https://openalex.org/W2789843538","https://openalex.org/W2883847355","https://openalex.org/W2904665340","https://openalex.org/W2923143097","https://openalex.org/W2971559821","https://openalex.org/W2979449748","https://openalex.org/W4214611987","https://openalex.org/W4236236547","https://openalex.org/W4247053599","https://openalex.org/W4254502766","https://openalex.org/W6601068097","https://openalex.org/W6679642144","https://openalex.org/W6683504902"],"related_works":["https://openalex.org/W2936184523","https://openalex.org/W4386926693","https://openalex.org/W4244035922","https://openalex.org/W4237970082","https://openalex.org/W2115140794","https://openalex.org/W2808875111","https://openalex.org/W4252732434","https://openalex.org/W2112284452","https://openalex.org/W924776604","https://openalex.org/W2041120224"],"abstract_inverted_index":{"The":[0],"FM-index":[1,23,43,71,121],"is":[2,94,124],"a":[3,32,38,61,69,78,98],"data":[4],"structure":[5],"used":[6],"in":[7,31],"genomics":[8],"for":[9,64,77],"exact":[10],"search":[11],"of":[12,41,55,82,111],"input":[13],"sequences":[14],"over":[15],"large":[16,56,65],"reference":[17,81],"genomes.":[18],"Algorithms":[19],"based":[20,89],"on":[21,90,96],"the":[22,42],"show":[24],"an":[25,103,119],"irregular":[26],"memory":[27,33,51],"access":[28],"pattern,":[29],"resulting":[30],"bound":[34],"problem.":[35],"We":[36,58,107],"analyze":[37],"recent":[39],"implementation":[40,54,122],"and":[44,102,113],"highlight":[45],"existing":[46],"throughput-memory":[47],"trade-offs,":[48],"showing":[49],"that":[50,123],"requirements":[52],"limit":[53],"k-steps.":[57],"propose":[59],"COFI,":[60],"COmpressed":[62],"FM-Index":[63],"K-steps.":[66],"COFI":[67],"enables":[68],"15-step":[70],"using":[72],"less":[73],"than":[74],"16":[75],"GB":[76],"human":[79],"genome":[80],"3":[83],"giga":[84],"base":[85],"pairs.":[86],"An":[87],"algorithm":[88],"this":[91],"new":[92],"layout":[93],"evaluated":[95],"both":[97],"Knights":[99],"Landing":[100],"(KNL)":[101],"Skylake-based":[104],"system":[105],"(SKX).":[106],"achieve":[108],"average":[109],"speed-ups":[110],"1.46\u00d7":[112],"1.39\u00d7,":[114],"respectively,":[115],"with":[116],"respect":[117],"to":[118],"state-of-the-art":[120],"already":[125],"well":[126],"optimized.":[127]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-05-09T13:55:54.758798","created_date":"2025-10-10T00:00:00"}