{"id":"https://openalex.org/W2565355131","doi":"https://doi.org/10.1093/bioinformatics/btw742","title":"Training alignment parameters for arbitrary sequencers with LAST-TRAIN","display_name":"Training alignment parameters for arbitrary sequencers with LAST-TRAIN","publication_year":2016,"publication_date":"2016-11-19","ids":{"openalex":"https://openalex.org/W2565355131","doi":"https://doi.org/10.1093/bioinformatics/btw742","mag":"2565355131","pmid":"https://pubmed.ncbi.nlm.nih.gov/28039163"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw742","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw742","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/6/926/25147844/btw742.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/6/926/25147844/btw742.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025857432","display_name":"Michiaki Hamada","orcid":"https://orcid.org/0000-0001-9466-1034"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]},{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Michiaki Hamada","raw_affiliation_strings":["Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan","Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan","Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N\u201306\u201310, 3\u20134\u20131, Okubo Shinjuku-ku, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N\u201306\u201310, 3\u20134\u20131, Okubo Shinjuku-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I150744194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028069650","display_name":"Yukiteru Ono","orcid":null},"institutions":[{"id":"https://openalex.org/I4210165074","display_name":"Information and Mathematical Science and Bioinformatics (Japan)","ror":"https://ror.org/05rgpb984","country_code":"JP","type":"company","lineage":["https://openalex.org/I4210165074"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yukiteru Ono","raw_affiliation_strings":["IMSBIO Co, Ltd, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"IMSBIO Co, Ltd, Tokyo, Japan","institution_ids":["https://openalex.org/I4210165074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082068847","display_name":"Kiyoshi Asai","orcid":"https://orcid.org/0000-0003-0909-4982"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kiyoshi Asai","raw_affiliation_strings":["Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan","Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan"],"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055829507","display_name":"Martin C. Frith","orcid":"https://orcid.org/0000-0003-0998-2859"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Martin C Frith","raw_affiliation_strings":["Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan","Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan","Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan"],"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5025857432","https://openalex.org/A5055829507"],"corresponding_institution_ids":["https://openalex.org/I150744194","https://openalex.org/I73613424","https://openalex.org/I74801974"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.1682,"has_fulltext":false,"cited_by_count":96,"citation_normalized_percentile":{"value":0.94596635,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"33","issue":"6","first_page":"926","last_page":"928"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7668967247009277},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.7110468149185181},{"id":"https://openalex.org/keywords/dna-sequencer","display_name":"DNA sequencer","score":0.6361732482910156},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.6146445274353027},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5635498762130737},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5357709527015686},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.513372540473938},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.46401891112327576},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.45033931732177734},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4472804069519043},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.413216769695282},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3824918866157532},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.2754925489425659},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.1700543463230133},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.1453981101512909},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14044460654258728},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11224567890167236},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10411122441291809}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7668967247009277},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.7110468149185181},{"id":"https://openalex.org/C70712619","wikidata":"https://www.wikidata.org/wiki/Q908889","display_name":"DNA sequencer","level":4,"score":0.6361732482910156},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.6146445274353027},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5635498762130737},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5357709527015686},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.513372540473938},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46401891112327576},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.45033931732177734},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4472804069519043},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.413216769695282},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3824918866157532},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2754925489425659},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.1700543463230133},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.1453981101512909},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14044460654258728},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11224567890167236},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10411122441291809},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0}],"mesh":[{"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":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw742","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw742","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/6/926/25147844/btw742.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28039163","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28039163","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:europepmc.org:4208737","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5351549","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw742","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw742","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/6/926/25147844/btw742.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320312414","display_name":"Oxford Nanopore Technologies","ror":"https://ror.org/04hyfx005"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2565355131.pdf","grobid_xml":"https://content.openalex.org/works/W2565355131.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W2007772656","https://openalex.org/W2009570821","https://openalex.org/W2016453697","https://openalex.org/W2037909948","https://openalex.org/W2053276922","https://openalex.org/W2110172970","https://openalex.org/W2137759177","https://openalex.org/W2158714788","https://openalex.org/W2162786061","https://openalex.org/W2164624668","https://openalex.org/W2171154262","https://openalex.org/W2337261418","https://openalex.org/W2397956000","https://openalex.org/W2576312521","https://openalex.org/W2611102567","https://openalex.org/W4240870042","https://openalex.org/W4245668478","https://openalex.org/W6663916349"],"related_works":["https://openalex.org/W2602845639","https://openalex.org/W2887783619","https://openalex.org/W2900530048","https://openalex.org/W4320503067","https://openalex.org/W2794729690","https://openalex.org/W4367176272","https://openalex.org/W4249076795","https://openalex.org/W2082825869","https://openalex.org/W2051969447","https://openalex.org/W2765704973"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":7}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
