{"id":"https://openalex.org/W2393535458","doi":"https://doi.org/10.1093/nar/gkw413","title":"tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes","display_name":"tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes","publication_year":2016,"publication_date":"2016-05-12","ids":{"openalex":"https://openalex.org/W2393535458","doi":"https://doi.org/10.1093/nar/gkw413","mag":"2393535458","pmid":"https://pubmed.ncbi.nlm.nih.gov/27174935"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkw413","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw413","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W54/7634746/gkw413.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/44/W1/W54/7634746/gkw413.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016860853","display_name":"Todd M. Lowe","orcid":"https://orcid.org/0000-0003-3253-6021"},"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":"Todd M. Lowe","raw_affiliation_strings":["Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA lowe@soe.ucsc.edu","Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA lowe@soe.ucsc.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"last","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":false,"raw_author_name":"Patricia P. Chan","raw_affiliation_strings":["Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5016860853"],"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":102.1677,"has_fulltext":true,"cited_by_count":2897,"citation_normalized_percentile":{"value":0.99985314,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"44","issue":"W1","first_page":"W54","last_page":"W57"},"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/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"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9994999766349792,"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":0.8152642250061035},{"id":"https://openalex.org/keywords/transfer-rna","display_name":"Transfer RNA","score":0.7716344594955444},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.6469106078147888},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6265122890472412},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6227589249610901},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.5982995629310608},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5845282673835754},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.569040834903717},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5283858180046082},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5179956555366516},{"id":"https://openalex.org/keywords/gene-nomenclature","display_name":"Gene nomenclature","score":0.4620589017868042},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4147201478481293},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4047909677028656}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8152642250061035},{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.7716344594955444},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.6469106078147888},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6265122890472412},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6227589249610901},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.5982995629310608},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5845282673835754},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.569040834903717},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5283858180046082},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5179956555366516},{"id":"https://openalex.org/C62177273","wikidata":"https://www.wikidata.org/wiki/Q5531556","display_name":"Gene nomenclature","level":4,"score":0.4620589017868042},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4147201478481293},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4047909677028656},{"id":"https://openalex.org/C514705636","wikidata":"https://www.wikidata.org/wiki/Q863247","display_name":"Nomenclature","level":3,"score":0.0},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"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":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/nar/gkw413","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw413","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W54/7634746/gkw413.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:27174935","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27174935","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:escholarship.org:ark:/13030/qt9z3114zv","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/9z3114zv","pdf_url":"https://escholarship.org/content/qt9z3114zv/qt9z3114zv.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, vol 44, iss W1","raw_type":"article"},{"id":"pmh:ark:/13030/qt9z3114zv","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt5fb8q49k","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/5fb8q49k","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, vol 44, iss W1","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3952923","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4987944","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"},{"id":"pmh:oai:open-archive.highwire.org:nar:44/W1/W54","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/44/W1/W54","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/nar/gkw413","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw413","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W54/7634746/gkw413.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":[],"awards":[{"id":"https://openalex.org/G4380074315","display_name":null,"funder_award_id":"HG006753","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2393535458.pdf","grobid_xml":"https://content.openalex.org/works/W2393535458.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1968392778","https://openalex.org/W2033713984","https://openalex.org/W2036649644","https://openalex.org/W2057892106","https://openalex.org/W2128868208","https://openalex.org/W2141152740","https://openalex.org/W2149429041","https://openalex.org/W2159207970","https://openalex.org/W2170487262","https://openalex.org/W2176686025","https://openalex.org/W2223836536","https://openalex.org/W4250052351"],"related_works":["https://openalex.org/W3111061871","https://openalex.org/W2099626126","https://openalex.org/W1999129612","https://openalex.org/W2059565715","https://openalex.org/W2116418175","https://openalex.org/W2127546476","https://openalex.org/W2042690128","https://openalex.org/W2152320398","https://openalex.org/W2148600978","https://openalex.org/W4309908782"],"abstract_inverted_index":{"High-throughput":[0],"genome":[1,11,106,111],"sequencing":[2],"continues":[3],"to":[4],"grow":[5],"the":[6,17,32,48,71,96,101],"need":[7],"for":[8],"rapid,":[9],"accurate":[10],"annotation":[12],"and":[13,39,64,103],"tRNA":[14,36,51,55,80],"genes":[15,99],"constitute":[16],"largest":[18],"family":[19],"of":[20,47,61,70],"essential,":[21],"ever-present":[22],"non-coding":[23],"RNA":[24],"genes.":[25],"Newly":[26],"developed":[27],"tRNAscan-SE":[28,72,114],"2.0":[29],"has":[30],"advanced":[31],"state-of-the-art":[33],"methodology":[34],"in":[35,79,100],"gene":[37],"detection":[38,56],"functional":[40],"prediction,":[41],"captured":[42],"by":[43,109],"rich":[44,105],"new":[45],"content":[46],"companion":[49],"Genomic":[50],"Database.":[52],"Previously,":[53],"web-server":[54],"was":[57],"isolated":[58],"from":[59],"knowledge":[60],"existing":[62],"tRNAs":[63],"their":[65],"annotation.":[66],"In":[67],"this":[68],"update":[69],"On-line":[73,115],"resource,":[74],"we":[75],"tie":[76],"together":[77],"improvements":[78],"classification":[81],"with":[82],"greatly":[83],"enhanced":[84],"biological":[85],"context":[86,107],"via":[87],"dynamically":[88],"generated":[89],"links":[90],"between":[91],"web":[92,116],"server":[93,117],"search":[94],"results,":[95],"most":[97],"relevant":[98],"GtRNAdb":[102],"interactive,":[104],"provided":[108],"UCSC":[110],"browsers.":[112],"The":[113],"can":[118],"be":[119],"accessed":[120],"at":[121],"http://trna.ucsc.edu/tRNAscan-SE/.":[122]},"counts_by_year":[{"year":2026,"cited_by_count":85},{"year":2025,"cited_by_count":215},{"year":2024,"cited_by_count":312},{"year":2023,"cited_by_count":301},{"year":2022,"cited_by_count":405},{"year":2021,"cited_by_count":522},{"year":2020,"cited_by_count":456},{"year":2019,"cited_by_count":379},{"year":2018,"cited_by_count":172},{"year":2017,"cited_by_count":43},{"year":2016,"cited_by_count":2}],"updated_date":"2026-07-04T07:58:01.006859","created_date":"2025-10-10T00:00:00"}
