{"id":"https://openalex.org/W2946131674","doi":"https://doi.org/10.1093/nar/gkz438","title":"tRNAviz: explore and visualize tRNA sequence features","display_name":"tRNAviz: explore and visualize tRNA sequence features","publication_year":2019,"publication_date":"2019-05-23","ids":{"openalex":"https://openalex.org/W2946131674","doi":"https://doi.org/10.1093/nar/gkz438","mag":"2946131674","pmid":"https://pubmed.ncbi.nlm.nih.gov/31127306"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkz438","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz438","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W542/28879847/gkz438.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","license_id":"https://openalex.org/licenses/cc-by","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/47/W1/W542/28879847/gkz438.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053524413","display_name":"Brian Y Lin","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":"Brian Y Lin","raw_affiliation_strings":["Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","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"],"affiliations":[{"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/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"],"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":3,"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":0.9376,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.74030103,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"47","issue":"W1","first_page":"W542","last_page":"W547"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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":0.9997000098228455,"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":0.9987999796867371,"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":0.9435911178588867},{"id":"https://openalex.org/keywords/transfer-rna","display_name":"Transfer RNA","score":0.7085541486740112},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5838209986686707},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5611293315887451},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4782668352127075},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.4358952045440674},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4345482289791107},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.19462671875953674},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.177130788564682},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13609999418258667}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9435911178588867},{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.7085541486740112},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5838209986686707},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5611293315887451},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4782668352127075},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.4358952045440674},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4345482289791107},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.19462671875953674},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.177130788564682},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13609999418258667}],"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":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000145","qualifier_name":"classification","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":"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":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019642","descriptor_name":"RNA, Archaeal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019642","descriptor_name":"RNA, Archaeal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019642","descriptor_name":"RNA, Archaeal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkz438","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz438","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W542/28879847/gkz438.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:31127306","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31127306","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/qt1n80c63p","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/1n80c63p","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, vol 47, iss W1","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5577273","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6602477","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkz438","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz438","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W542/28879847/gkz438.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","license_id":"https://openalex.org/licenses/cc-by","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/G3011145040","display_name":null,"funder_award_id":"R01HG006753","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"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2946131674.pdf","grobid_xml":"https://content.openalex.org/works/W2946131674.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1973290333","https://openalex.org/W1974275894","https://openalex.org/W1983859619","https://openalex.org/W1995314607","https://openalex.org/W2001394720","https://openalex.org/W2011368877","https://openalex.org/W2013039688","https://openalex.org/W2014456355","https://openalex.org/W2038379310","https://openalex.org/W2043477093","https://openalex.org/W2057892106","https://openalex.org/W2065920317","https://openalex.org/W2072091744","https://openalex.org/W2083691392","https://openalex.org/W2112284944","https://openalex.org/W2141152740","https://openalex.org/W2142584500","https://openalex.org/W2149429041","https://openalex.org/W2154759788","https://openalex.org/W2162520906","https://openalex.org/W2167673850","https://openalex.org/W2223836536","https://openalex.org/W2336330109","https://openalex.org/W2393535458","https://openalex.org/W2742512275","https://openalex.org/W2751076435","https://openalex.org/W2782314590","https://openalex.org/W4233142859","https://openalex.org/W4250052351","https://openalex.org/W4252182636"],"related_works":["https://openalex.org/W2040216736","https://openalex.org/W1998434095","https://openalex.org/W1979806605","https://openalex.org/W2075273261","https://openalex.org/W2939643004","https://openalex.org/W1971406113","https://openalex.org/W2082063162","https://openalex.org/W2054735031","https://openalex.org/W1972846730","https://openalex.org/W4245380020"],"abstract_inverted_index":{"Transfer":[0],"RNAs":[1],"(tRNAs)":[2],"are":[3,47,136],"ubiquitous":[4],"across":[5],"the":[6,57],"tree":[7],"of":[8,42,61,68,78,93],"life.":[9],"Although":[10],"tRNA":[11,54,79,104,129],"structure":[12],"is":[13,17,65,143],"highly":[14],"conserved,":[15],"there":[16,64],"still":[18],"significant":[19],"variation":[20,31],"in":[21,53],"sequence":[22,80,105,114,119],"features":[23,115],"between":[24],"clades,":[25],"isotypes":[26],"and":[27,73,102,116,125,138],"even":[28],"isodecoders.":[29],"This":[30],"not":[32],"only":[33],"impacts":[34],"translation,":[35],"but":[36],"as":[37,132],"shown":[38],"by":[39,122],"a":[40,66,97,109],"variety":[41],"recent":[43],"studies,":[44],"nontranslation-associated":[45],"functions":[46],"also":[48],"sensitive":[49],"to":[50],"small":[51],"changes":[52],"sequence.":[55],"Despite":[56],"rapidly":[58],"growing":[59],"number":[60],"sequenced":[62],"genomes,":[63],"lack":[67],"tools":[69],"for":[70,100,111],"both":[71],"small-":[72],"large-scale":[74],"comparative":[75],"genomics":[76],"analysis":[77],"features.":[81,106],"Here,":[82],"we":[83],"have":[84],"integrated":[85],"over":[86],"150":[87],"000":[88],"tRNAs":[89],"spanning":[90],"all":[91],"domains":[92],"life":[94],"into":[95],"tRNAviz,":[96],"web":[98,141],"application":[99],"exploring":[101],"visualizing":[103],"tRNAviz":[107],"implements":[108],"framework":[110],"determining":[112],"consensus":[113],"can":[117],"generate":[118],"feature":[120],"distributions":[121],"isotypes,":[123],"clades":[124],"anticodons,":[126],"among":[127],"other":[128],"properties":[130],"such":[131],"score.":[133],"All":[134],"visualizations":[135],"interactive":[137],"exportable.":[139],"The":[140],"server":[142],"publicly":[144],"available":[145],"at":[146],"http://trna.ucsc.edu/tRNAviz/.":[147]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
