{"id":"https://openalex.org/W2036649644","doi":"https://doi.org/10.1093/nar/gkn787","title":"GtRNAdb: a database of transfer RNA genes detected in genomic sequence","display_name":"GtRNAdb: a database of transfer RNA genes detected in genomic sequence","publication_year":2008,"publication_date":"2008-11-05","ids":{"openalex":"https://openalex.org/W2036649644","doi":"https://doi.org/10.1093/nar/gkn787","mag":"2036649644","pmid":"https://pubmed.ncbi.nlm.nih.gov/18984615"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkn787","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn787","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_1/D93/3289033/gkn787.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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://academic.oup.com/nar/article-pdf/37/suppl_1/D93/3289033/gkn787.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081056569","display_name":"Patricia P. Chan","orcid":"https://orcid.org/0000-0003-0810-1642"},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"P. P. Chan","raw_affiliation_strings":["Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, SOE-2, Santa Cruz, CA 95064, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, SOE-2, Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007132238","display_name":"T. M. Lowe","orcid":null},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. M. Lowe","raw_affiliation_strings":["Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, SOE-2, Santa Cruz, CA 95064, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, SOE-2, Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5081056569"],"corresponding_institution_ids":["https://openalex.org/I185103710"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":11.0031,"has_fulltext":true,"cited_by_count":902,"citation_normalized_percentile":{"value":0.98978579,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"37","issue":"Database","first_page":"D93","last_page":"D97"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9998999834060669,"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/T11482","display_name":"RNA modifications and cancer","score":0.9998999834060669,"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/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/T10521","display_name":"RNA and protein synthesis mechanisms","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"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.8528627157211304},{"id":"https://openalex.org/keywords/transfer-rna","display_name":"Transfer RNA","score":0.7108892202377319},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6852352619171143},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6592866778373718},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6504281759262085},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49447083473205566},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.45089462399482727},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.41765230894088745},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4138016700744629},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.3978625535964966},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.32402729988098145}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8528627157211304},{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.7108892202377319},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6852352619171143},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6592866778373718},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6504281759262085},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49447083473205566},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.45089462399482727},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.41765230894088745},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4138016700744629},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3978625535964966},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.32402729988098145},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"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":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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/gkn787","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn787","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_1/D93/3289033/gkn787.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:18984615","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18984615","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:2686519","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkn787","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkn787","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn787","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_1/D93/3289033/gkn787.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.4399999976158142,"display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309018","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71"},{"id":"https://openalex.org/F4320310688","display_name":"Center for Information Technology Research in the Interest of Society","ror":"https://ror.org/00zv0wd17"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2036649644.pdf","grobid_xml":"https://content.openalex.org/works/W2036649644.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1991398089","https://openalex.org/W2011368877","https://openalex.org/W2042881722","https://openalex.org/W2055043387","https://openalex.org/W2073321994","https://openalex.org/W2106695679","https://openalex.org/W2107903949","https://openalex.org/W2141885858","https://openalex.org/W2149429041","https://openalex.org/W2153173493","https://openalex.org/W2155869782","https://openalex.org/W2157613837","https://openalex.org/W2159995027","https://openalex.org/W2167673850","https://openalex.org/W2740984310","https://openalex.org/W4210323379","https://openalex.org/W4236236547"],"related_works":["https://openalex.org/W2168783124","https://openalex.org/W2040216736","https://openalex.org/W2126958666","https://openalex.org/W1998434095","https://openalex.org/W4243357985","https://openalex.org/W2105071916","https://openalex.org/W4312203868","https://openalex.org/W2012158738","https://openalex.org/W4229794866","https://openalex.org/W1759033142"],"abstract_inverted_index":{"Transfer":[0],"RNAs":[1],"(tRNAs)":[2],"represent":[3],"the":[4,21,38,48,113],"single":[5],"largest,":[6],"best-understood":[7],"class":[8],"of":[9,24,30,69,109,115],"non-protein":[10],"coding":[11],"RNA":[12],"genes":[13,31,58,71,111],"found":[14],"in":[15,112],"all":[16,116],"living":[17],"organisms.":[18],"By":[19],"far,":[20],"major":[22],"source":[23],"new":[25],"tRNAs":[26],"is":[27,137],"computational":[28],"identification":[29],"within":[32,72],"newly":[33],"sequenced":[34],"genomes.":[35],"To":[36],"organize":[37],"rapidly":[39],"growing":[40],"collection":[41],"and":[42,80,90,102],"enable":[43],"systematic":[44],"analyses,":[45],"we":[46],"created":[47],"Genomic":[49],"tRNA":[50,57,70,110,130],"Database":[51],"(GtRNAdb),":[52],"currently":[53],"including":[54,76],"over":[55],"74,000":[56],"predicted":[59],"from":[60],"740":[61],"species.":[62],"The":[63,121,135],"web":[64],"resource":[65],"provides":[66],"overview":[67],"statistics":[68],"each":[73,97],"analyzed":[74],"genome,":[75],"information":[77],"by":[78,126],"isotype":[79],"genetic":[81,119],"locus,":[82],"easily":[83],"downloadable":[84],"primary":[85,127],"sequences,":[86],"graphical":[87,107],"secondary":[88],"structures":[89],"multiple":[91],"sequence":[92,128],"alignments.":[93],"Direct":[94],"links":[95],"for":[96],"gene":[98],"to":[99],"UCSC":[100],"eukaryotic":[101],"microbial":[103],"genome":[104],"browsers":[105],"provide":[106],"display":[108],"context":[114],"other":[117],"local":[118],"information.":[120],"database":[122,136],"can":[123],"be":[124],"searched":[125],"similarity,":[129],"characteristics":[131],"or":[132],"phylogenetic":[133],"group.":[134],"publicly":[138],"available":[139],"at":[140],"http://gtrnadb.ucsc.edu.":[141]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":47},{"year":2024,"cited_by_count":56},{"year":2023,"cited_by_count":48},{"year":2022,"cited_by_count":43},{"year":2021,"cited_by_count":57},{"year":2020,"cited_by_count":52},{"year":2019,"cited_by_count":54},{"year":2018,"cited_by_count":62},{"year":2017,"cited_by_count":75},{"year":2016,"cited_by_count":79},{"year":2015,"cited_by_count":78},{"year":2014,"cited_by_count":66},{"year":2013,"cited_by_count":56},{"year":2012,"cited_by_count":40}],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2025-10-10T00:00:00"}
