{"id":"https://openalex.org/W4415780105","doi":"https://doi.org/10.1093/bioinformatics/btag183","title":"Singletrack: an algorithm for improving memory consumption and performance of gap-affine sequence alignment","display_name":"Singletrack: an algorithm for improving memory consumption and performance of gap-affine sequence alignment","publication_year":2026,"publication_date":"2026-04-10","ids":{"openalex":"https://openalex.org/W4415780105","doi":"https://doi.org/10.1093/bioinformatics/btag183","pmid":"https://pubmed.ncbi.nlm.nih.gov/41981735"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag183","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag183","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"preprint","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag183","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073353754","display_name":"Lori\u00e9n L\u00f3pez\u2010Villellas","orcid":"https://orcid.org/0000-0002-1891-4359"},"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":"Lori\u00e9n L\u00f3pez-Villellas","raw_affiliation_strings":["Departamento de Inform\u00e1tica e Ingenier\u00eda de Sistemas/Arag\u00f3n Institute for Engineering Research (I3A), Universidad de Zaragoza , Zaragoza, 50018,"],"raw_orcid":"https://orcid.org/0000-0002-1891-4359","affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica e Ingenier\u00eda de Sistemas/Arag\u00f3n Institute for Engineering Research (I3A), Universidad de Zaragoza , Zaragoza, 50018,","institution_ids":["https://openalex.org/I255234318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5099980861","display_name":"Cristian I\u00f1iguez","orcid":"https://orcid.org/0009-0000-8950-2776"},"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":"Cristian I\u00f1iguez","raw_affiliation_strings":["Barcelona Supercomputing Center , Barcelona, 08034,"],"raw_orcid":"https://orcid.org/0009-0000-8950-2776","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center , Barcelona, 08034,","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120224061","display_name":"Albert Jim\u00e9nez-Blanco","orcid":"https://orcid.org/0009-0008-3958-9664"},"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":"Albert Jim\u00e9nez-Blanco","raw_affiliation_strings":["Barcelona Supercomputing Center , Barcelona, 08034,","Department of Computer Science, Universitat Polit\u00e8cnica de Catalunya , Barcelona, 08034,"],"raw_orcid":"https://orcid.org/0009-0008-3958-9664","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center , Barcelona, 08034,","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"Department of Computer Science, Universitat Polit\u00e8cnica de Catalunya , Barcelona, 08034,","institution_ids":["https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005302308","display_name":"Quim Aguado-Puig","orcid":"https://orcid.org/0000-0003-4871-3192"},"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":"Quim Aguado-Puig","raw_affiliation_strings":["Departament d\u2019Arquitectura de Computadors i Sistemes Operatius, Universitat Aut\u00f2noma de Barcelona , Barcelona, 08193,"],"raw_orcid":"https://orcid.org/0000-0003-4871-3192","affiliations":[{"raw_affiliation_string":"Departament d\u2019Arquitectura de Computadors i Sistemes Operatius, Universitat Aut\u00f2noma de Barcelona , Barcelona, 08193,","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"middle","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 Moret\u00f3","raw_affiliation_strings":["Barcelona Supercomputing Center , Barcelona, 08034,","Department of Computer Science, Universitat Polit\u00e8cnica de Catalunya , Barcelona, 08034,"],"raw_orcid":"https://orcid.org/0000-0002-9848-8758","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center , Barcelona, 08034,","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"Department of Computer Science, Universitat Polit\u00e8cnica de Catalunya , Barcelona, 08034,","institution_ids":["https://openalex.org/I9617848"]}]},{"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":"Jes\u00fas Alastruey-Bened\u00e9","raw_affiliation_strings":["Departamento de Inform\u00e1tica e Ingenier\u00eda de Sistemas/Arag\u00f3n Institute for Engineering Research (I3A), Universidad de Zaragoza , Zaragoza, 50018,"],"raw_orcid":"https://orcid.org/0000-0003-4164-5078","affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica e Ingenier\u00eda de Sistemas/Arag\u00f3n Institute for Engineering Research (I3A), Universidad de Zaragoza , Zaragoza, 50018,","institution_ids":["https://openalex.org/I255234318"]}]},{"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 Ib\u00e1\u00f1ez","raw_affiliation_strings":["Departamento de Inform\u00e1tica e Ingenier\u00eda de Sistemas/Arag\u00f3n Institute for Engineering Research (I3A), Universidad de Zaragoza , Zaragoza, 50018,"],"raw_orcid":"https://orcid.org/0000-0002-5916-7898","affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica e Ingenier\u00eda de Sistemas/Arag\u00f3n Institute for Engineering Research (I3A), Universidad de Zaragoza , Zaragoza, 50018,","institution_ids":["https://openalex.org/I255234318"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052502603","display_name":"Santiago Marco\u2010Sola","orcid":"https://orcid.org/0000-0001-7951-3914"},"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":"Santiago Marco-Sola","raw_affiliation_strings":["Barcelona Supercomputing Center , Barcelona, 08034,","Department of Computer Science, Universitat Polit\u00e8cnica de Catalunya , Barcelona, 08034,"],"raw_orcid":"https://orcid.org/0000-0001-7951-3914","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center , Barcelona, 08034,","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"Department of Computer Science, Universitat Polit\u00e8cnica de Catalunya , Barcelona, 08034,","institution_ids":["https://openalex.org/I9617848"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.1191,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.88830742,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"42","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5342000126838684,"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":0.5342000126838684,"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":0.1656000018119812,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.1378999948501587,"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/bottleneck","display_name":"Bottleneck","score":0.6601999998092651},{"id":"https://openalex.org/keywords/dual","display_name":"Dual (grammatical number)","score":0.5734999775886536},{"id":"https://openalex.org/keywords/memory-hierarchy","display_name":"Memory hierarchy","score":0.5389999747276306},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4431999921798706},{"id":"https://openalex.org/keywords/memory-management","display_name":"Memory management","score":0.42419999837875366},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.4036000072956085},{"id":"https://openalex.org/keywords/reduction","display_name":"Reduction (mathematics)","score":0.37549999356269836},{"id":"https://openalex.org/keywords/out-of-core-algorithm","display_name":"Out-of-core algorithm","score":0.30979999899864197},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.29829999804496765}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7982000112533569},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.6601999998092651},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6050000190734863},{"id":"https://openalex.org/C2780980858","wikidata":"https://www.wikidata.org/wiki/Q110022","display_name":"Dual (grammatical number)","level":2,"score":0.5734999775886536},{"id":"https://openalex.org/C2778100165","wikidata":"https://www.wikidata.org/wiki/Q1589327","display_name":"Memory hierarchy","level":3,"score":0.5389999747276306},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4431999921798706},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4302000105381012},{"id":"https://openalex.org/C176649486","wikidata":"https://www.wikidata.org/wiki/Q2308807","display_name":"Memory management","level":3,"score":0.42419999837875366},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.4036000072956085},{"id":"https://openalex.org/C111335779","wikidata":"https://www.wikidata.org/wiki/Q3454686","display_name":"Reduction (mathematics)","level":2,"score":0.37549999356269836},{"id":"https://openalex.org/C79470037","wikidata":"https://www.wikidata.org/wiki/Q279748","display_name":"Out-of-core algorithm","level":2,"score":0.30979999899864197},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.29829999804496765},{"id":"https://openalex.org/C57863822","wikidata":"https://www.wikidata.org/wiki/Q905488","display_name":"Flat memory model","level":4,"score":0.2937999963760376},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.2881999909877777},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.2856999933719635},{"id":"https://openalex.org/C78548338","wikidata":"https://www.wikidata.org/wiki/Q2493","display_name":"Data compression","level":2,"score":0.2833999991416931},{"id":"https://openalex.org/C106516650","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm design","level":2,"score":0.28209999203681946},{"id":"https://openalex.org/C17349429","wikidata":"https://www.wikidata.org/wiki/Q1049914","display_name":"Matrix multiplication","level":3,"score":0.2784999907016754},{"id":"https://openalex.org/C92855701","wikidata":"https://www.wikidata.org/wiki/Q5830907","display_name":"Computer memory","level":3,"score":0.2759999930858612},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.2754000127315521},{"id":"https://openalex.org/C82687282","wikidata":"https://www.wikidata.org/wiki/Q66221","display_name":"Auxiliary memory","level":2,"score":0.27300000190734863},{"id":"https://openalex.org/C2781357197","wikidata":"https://www.wikidata.org/wiki/Q5757597","display_name":"High memory","level":2,"score":0.2709999978542328},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.26899999380111694},{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.26600000262260437},{"id":"https://openalex.org/C133875982","wikidata":"https://www.wikidata.org/wiki/Q764810","display_name":"Shared memory","level":2,"score":0.2612000107765198},{"id":"https://openalex.org/C2778915421","wikidata":"https://www.wikidata.org/wiki/Q3643177","display_name":"Performance improvement","level":2,"score":0.25440001487731934},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2531000077724457},{"id":"https://openalex.org/C91481028","wikidata":"https://www.wikidata.org/wiki/Q1054686","display_name":"Distributed memory","level":3,"score":0.25220000743865967},{"id":"https://openalex.org/C118702147","wikidata":"https://www.wikidata.org/wiki/Q189396","display_name":"Dynamic random-access memory","level":3,"score":0.2508000135421753}],"mesh":[{"descriptor_ui":"D000098433","descriptor_name":"Dynamic Programming","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btag183","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag183","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.1101/2025.10.31.685625","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.10.31.685625","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/11/02/2025.10.31.685625.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:41981735","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41981735","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:13171181","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13171181/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:upcommons.upc.edu:2117/462692","is_oa":true,"landing_page_url":"https://hdl.handle.net/2117/462692","pdf_url":null,"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"},{"id":"pmh:oai:zaguan.unizar.es:171694","is_oa":true,"landing_page_url":"http://zaguan.unizar.es/record/171694","pdf_url":null,"source":{"id":"https://openalex.org/S4306401812","display_name":"Zaguan (University of Zaragoza Repository)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I255234318","host_organization_name":"Universidad de Zaragoza","host_organization_lineage":["https://openalex.org/I255234318"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag183","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag183","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1162263618","display_name":null,"funder_award_id":"PID2020-113614RB-C21","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G121809054","display_name":null,"funder_award_id":"MCIN/AEI/10","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G1432709775","display_name":null,"funder_award_id":"E45_20R","funder_id":"https://openalex.org/F4320326208","funder_display_name":"Gobierno de Arag\u00f3n"},{"id":"https://openalex.org/G1527750938","display_name":null,"funder_award_id":"PID2023-146193OB-I00","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G1643949827","display_name":null,"funder_award_id":"AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G1787381284","display_name":null,"funder_award_id":"T58_23R","funder_id":"https://openalex.org/F4320326208","funder_display_name":"Gobierno de Arag\u00f3n"},{"id":"https://openalex.org/G1793925083","display_name":"3D Decision Support Tool for Brain Tumor Surgery","funder_award_id":"101137416","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2064873908","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G2262748287","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G2309174360","display_name":null,"funder_award_id":"10.13039","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G2360082399","display_name":null,"funder_award_id":"PID2023-146193OB-I00","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G2601397997","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2825053243","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320326208","funder_display_name":"Gobierno de Arag\u00f3n"},{"id":"https://openalex.org/G2893052478","display_name":null,"funder_award_id":"TSI-069100-2023-0015","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3005324705","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G300979063","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3020948319","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320326208","funder_display_name":"Gobierno de Arag\u00f3n"},{"id":"https://openalex.org/G3219925899","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3480869486","display_name":null,"funder_award_id":"13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3681454997","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4017095837","display_name":null,"funder_award_id":"AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G4042783231","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4290597678","display_name":null,"funder_award_id":"PID2020-113614RB-C21","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4337097655","display_name":null,"funder_award_id":"2021-SGR-00574","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G464105488","display_name":null,"funder_award_id":"PID2023","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G4873200889","display_name":null,"funder_award_id":"PID2023-146193OB-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G4976336944","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G5080475149","display_name":null,"funder_award_id":"10.13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G5421974903","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G5550858994","display_name":null,"funder_award_id":"AEI/10","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G5635532810","display_name":null,"funder_award_id":"13039","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G5805502524","display_name":null,"funder_award_id":"PID2020","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G6394188553","display_name":null,"funder_award_id":"PID2022-136454NB-C22","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G6558061132","display_name":null,"funder_award_id":"MCIN/AEI/10.","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G6589649124","display_name":null,"funder_award_id":"PID2020-","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G6731524417","display_name":null,"funder_award_id":"PID2020","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G6823456974","display_name":null,"funder_award_id":"AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7084143925","display_name":null,"funder_award_id":"AEI/10","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7140199198","display_name":null,"funder_award_id":"E45_20R T58_23R","funder_id":"https://openalex.org/F4320326208","funder_display_name":"Gobierno de Arag\u00f3n"},{"id":"https://openalex.org/G7186414377","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G7266728691","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7535663061","display_name":null,"funder_award_id":"AEI/10.","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7624076277","display_name":null,"funder_award_id":"PID2023-146511NB-I00","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7643708868","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G768701810","display_name":null,"funder_award_id":"2021-SGR-00763","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G7805626310","display_name":null,"funder_award_id":"10.13039","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G8055432103","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G8118709007","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320334322","funder_display_name":"HORIZON EUROPE Framework Programme"},{"id":"https://openalex.org/G8208931781","display_name":null,"funder_award_id":"T58_23R","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G836255325","display_name":null,"funder_award_id":"PID2020-113614RB-C21","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G8695128545","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8853601691","display_name":null,"funder_award_id":"/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G8872346354","display_name":null,"funder_award_id":"MCIN/AEI/10.13039","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G8920660035","display_name":null,"funder_award_id":"PID2022","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320315062","display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades","ror":null},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321505","display_name":"Generalitat de Catalunya","ror":"https://ror.org/01bg62x04"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320326208","display_name":"Gobierno de Arag\u00f3n","ror":"https://ror.org/0425pg203"},{"id":"https://openalex.org/F4320334322","display_name":"HORIZON EUROPE Framework Programme","ror":null},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1973530293","https://openalex.org/W2011632873","https://openalex.org/W2068448872","https://openalex.org/W2074774389","https://openalex.org/W2100751585","https://openalex.org/W2158714788","https://openalex.org/W2165654401","https://openalex.org/W2194172909","https://openalex.org/W2260037449","https://openalex.org/W2396849069","https://openalex.org/W2607669908","https://openalex.org/W2788876413","https://openalex.org/W2789843538","https://openalex.org/W2941874147","https://openalex.org/W3046494740","https://openalex.org/W3159082119","https://openalex.org/W3193844559","https://openalex.org/W4200042858","https://openalex.org/W4224278121","https://openalex.org/W4253539230","https://openalex.org/W4292240213","https://openalex.org/W4319334382","https://openalex.org/W4403609447"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Advances":[1],"in":[2,8,16,101,204,224,240],"DNA":[3],"sequencing":[4],"have":[5],"outpaced":[6],"advances":[7],"computation,":[9],"making":[10],"sequence":[11],"alignment":[12,46,72],"a":[13,65,117,221],"major":[14],"bottleneck":[15],"genome":[17],"data":[18],"analyses.":[19],"Classical":[20],"dynamic":[21],"programming":[22],"(DP)":[23],"algorithms":[24,125],"are":[25,243],"particularly":[26],"memory-intensive,":[27],"especially":[28],"when":[29],"computing":[30],"gap-affine":[31,34,57,60,90,167,170],"and":[32,58,91,109,126,133,149,157,159,164,168,249],"dual":[33,59,94,169],"alignments.":[35],"Existing":[36],"strategies":[37],"to":[38,75,83,186,209,229],"reduce":[39],"memory":[40,98,107,144,193,225],"consumption":[41,99,145],"often":[42],"sacrifice":[43],"speed":[44],"or":[45],"accuracy.":[47],"RESULTS:":[48],"We":[49,139],"present":[50],"Singletrack,":[51],"an":[52],"efficient":[53,211],"algorithm":[54],"for":[55,89,93,146,166,227],"backtrace":[56,119],"alignments":[61],"that":[62,141],"requires":[63],"storing":[64],"single":[66],"DP":[67,77],"matrix":[68],"while":[69,195],"preserving":[70],"optimal":[71],"results.":[73],"Compared":[74,208],"classical":[76],"algorithms,":[78,151],"Singletrack":[79,115,142,179,196,237],"removes":[80],"the":[81,106,130,134,189,198,201,210,215],"need":[82],"store":[84],"additional":[85],"matrices":[86],"(i.e.":[87],"2":[88],"4":[92],"gap-affine),":[95],"significantly":[96],"reducing":[97,103],"and,":[100],"turn,":[102],"pressure":[104],"on":[105,245],"hierarchy":[108],"improving":[110],"overall":[111],"performance.":[112,232],"Most":[113],"importantly,":[114],"is":[116],"general":[118],"method":[120],"compatible":[121],"with":[122,178],"state-of-the-art":[123],"DP-based":[124],"heuristics,":[127],"such":[128],"as":[129],"Suzuki-Kasahara":[131],"(SK)":[132],"Wavefront":[135],"Alignment":[136],"(WFA)":[137],"algorithms.":[138],"demonstrate":[140],"reduces":[143],"both":[147],"SK":[148,153,182],"WFA":[150,160,202,219],"lowering":[152],"usage":[154,161,226],"by":[155,162,184,206],"2\u00d7":[156],"4\u00d7":[158],"3\u00d7":[163],"5\u00d7":[165],"alignments,":[171],"respectively.":[172],"Moreover,":[173],"replacing":[174],"KSW2's":[175],"memory-reduction":[176],"technique":[177],"accelerates":[180],"its":[181],"implementation":[183,203],"up":[185,228],"1.4\u00d7":[187],"at":[188],"cost":[190],"of":[191,200,218],"doubling":[192],"consumption,":[194],"increases":[197],"performance":[199],"WFA2-lib":[205],"1.2-2.1\u00d7.":[207],"linear-memory":[212],"BiWFA":[213],"algorithm,":[214],"Singletrack-accelerated":[216],"version":[217],"trades":[220],"practical":[222],"increase":[223],"5.2\u00d7":[230],"higher":[231],"AVAILABILITY":[233],"AND":[234],"IMPLEMENTATION:":[235],"The":[236],"implementations":[238],"presented":[239],"this":[241],"work":[242],"available":[244],"Zenodo":[246],"(DOI:":[247],"10.5281/zenodo.18770585)":[248],"GitHub":[250],"(https://github.com/LorienLV/singletrack).":[251]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-11-03T00:00:00"}
