{"id":"https://openalex.org/W4246658119","doi":"https://doi.org/10.1093/nar/gkn692","title":"tRNADB-CE: tRNA gene database curated manually by experts","display_name":"tRNADB-CE: tRNA gene database curated manually by experts","publication_year":2008,"publication_date":"2008-10-08","ids":{"openalex":"https://openalex.org/W4246658119","doi":"https://doi.org/10.1093/nar/gkn692","pmid":"https://pubmed.ncbi.nlm.nih.gov/18842632"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkn692","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn692","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/nar/gkn692","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058213261","display_name":"Takashi Abe","orcid":"https://orcid.org/0000-0002-8692-4241"},"institutions":[{"id":"https://openalex.org/I194335595","display_name":"Nagahama Institute of Bio-Science and Technology","ror":"https://ror.org/03m5fme96","country_code":"JP","type":"education","lineage":["https://openalex.org/I194335595"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Takashi Abe","raw_affiliation_strings":["Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan. takaabe@nagahama-i-bio.ac.jp"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan. takaabe@nagahama-i-bio.ac.jp","institution_ids":["https://openalex.org/I194335595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021391751","display_name":"Toshimichi Ikemura","orcid":"https://orcid.org/0000-0001-9931-172X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Toshimichi Ikemura","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090342942","display_name":"Yasuo Ohara","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yasuo Ohara","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002236206","display_name":"Hiroshi Uehara","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hiroshi Uehara","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104534615","display_name":"Makoto Kinouchi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Makoto Kinouchi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046567908","display_name":"Shigehiko Kanaya","orcid":"https://orcid.org/0000-0002-2147-6900"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shigehiko Kanaya","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057076300","display_name":"Yuko Yamada","orcid":"https://orcid.org/0000-0001-5502-5895"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yuko Yamada","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028074922","display_name":"Akira Muto","orcid":"https://orcid.org/0000-0003-4276-1775"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Akira Muto","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5038350600","display_name":"Hachiro Inokuchi","orcid":"https://orcid.org/0000-0003-1708-7918"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hachiro Inokuchi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5058213261"],"corresponding_institution_ids":["https://openalex.org/I194335595"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.6844,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.83909249,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"suppl_1","first_page":"D163","last_page":"D168"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9991000294685364,"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/T11482","display_name":"RNA modifications and cancer","score":0.9984999895095825,"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/genome","display_name":"Genome","score":0.7729848623275757},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7635047435760498},{"id":"https://openalex.org/keywords/genbank","display_name":"GenBank","score":0.7298921942710876},{"id":"https://openalex.org/keywords/transfer-rna","display_name":"Transfer RNA","score":0.7142069935798645},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.7104986310005188},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5787967443466187},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5522255897521973},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.42093753814697266},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.4203181862831116},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40744853019714355},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.12293782830238342},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.06853920221328735}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7729848623275757},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7635047435760498},{"id":"https://openalex.org/C79029880","wikidata":"https://www.wikidata.org/wiki/Q901755","display_name":"GenBank","level":3,"score":0.7298921942710876},{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.7142069935798645},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.7104986310005188},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5787967443466187},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5522255897521973},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.42093753814697266},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.4203181862831116},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40744853019714355},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.12293782830238342},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.06853920221328735}],"mesh":[{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019766","descriptor_name":"Genes, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019766","descriptor_name":"Genes, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019766","descriptor_name":"Genes, Archaeal","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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkn692","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn692","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:18842632","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18842632","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2686568","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2686568","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkn692","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn692","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W183984956","https://openalex.org/W222250992","https://openalex.org/W1971824376","https://openalex.org/W1996053875","https://openalex.org/W2005568256","https://openalex.org/W2005942865","https://openalex.org/W2033060935","https://openalex.org/W2042881722","https://openalex.org/W2099991744","https://openalex.org/W2106882534","https://openalex.org/W2107580398","https://openalex.org/W2112389572","https://openalex.org/W2113601822","https://openalex.org/W2149429041","https://openalex.org/W2155319253","https://openalex.org/W2158714788","https://openalex.org/W2167673850","https://openalex.org/W2170487262","https://openalex.org/W4250052351","https://openalex.org/W4320800138","https://openalex.org/W4388364538"],"related_works":["https://openalex.org/W2773247701","https://openalex.org/W2951353021","https://openalex.org/W1969895229","https://openalex.org/W1560725704","https://openalex.org/W3047903919","https://openalex.org/W4386028668","https://openalex.org/W2045048100","https://openalex.org/W2132017020","https://openalex.org/W4321242349","https://openalex.org/W2112814626"],"abstract_inverted_index":{"We":[0],"constructed":[1],"a":[2],"new":[3],"large-scale":[4],"database":[5,106,128],"of":[6,14,57,61,71,74,111,119,121,131,148,157,163,181],"tRNA":[7,43,75,94,100,153,164,183],"genes":[8,44,101,113,123,165,177,184],"by":[9,47,90,126],"analyzing":[10],"534":[11],"complete":[12,132,159],"genomes":[13,19,82,133],"prokaryotes":[15],"and":[16,28,55,108,146,169,178],"394":[17],"draft":[18],"in":[20,26,92,104,174,185],"WGS":[21],"(Whole":[22],"Genome":[23],"Shotgun)":[24],"division":[25],"DDBJ/EMBL/GenBank":[27],"approximately":[29,69],"6.2":[30],"million":[31],"DNA":[32],"fragment":[33],"sequences":[34],"obtained":[35,78],"from":[36,79,129],"metagenomic":[37],"analyses.":[38],"This":[39],"exhaustive":[40],"search":[41],"for":[42,68,140,166],"was":[45,114],"performed":[46],"running":[48],"three":[49,64],"computer":[50],"programs":[51,65],"to":[52],"enhance":[53],"completeness":[54],"accuracy":[56],"the":[58,72,93,105,109,112,122,127,158,161,170,179],"prediction.":[59],"Discordances":[60],"assignment":[62],"among":[63,151],"were":[66,87,102],"found":[67],"4%":[70],"total":[73],"gene":[76],"candidates":[77],"these":[80],"prokaryote":[81],"analyzed.":[83],"The":[84,137],"discordant":[85],"cases":[86],"manually":[88],"checked":[89],"experts":[91],"experimental":[95],"field.":[96],"In":[97],"total,":[98],"144,061":[99],"registered":[103],"'tRNADB-CE',":[107],"number":[110,162],"more":[115],"than":[116],"four":[117],"times":[118],"that":[120],"previously":[124],"reported":[125],"analyses":[130],"with":[134],"tRNAscan-SE":[135],"program.":[136],"tRNADB-CE":[138,191],"allows":[139],"browsing":[141],"sequence":[142],"information,":[143],"cloverleaf":[144],"structures":[145],"results":[147],"similarity":[149],"searches":[150],"all":[152,175],"genes.":[154],"For":[155],"each":[156,186],"genomes,":[160],"individual":[167,182],"anticodons":[168],"codon":[171],"usage":[172],"frequency":[173],"protein":[176],"positioning":[180],"genome":[187],"can":[188,192],"be":[189,193],"browsed.":[190],"accessed":[194],"freely":[195],"at":[196],"http://trna.nagahama-i-bio.ac.jp.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-20T08:49:12.498775","created_date":"2025-10-10T00:00:00"}