{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T01:28:13Z","timestamp":1768440493516,"version":"3.49.0"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2019,5,25]],"date-time":"2019-05-25T00:00:00Z","timestamp":1558742400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG006753"],"award-info":[{"award-number":["R01HG006753"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Transfer RNAs (tRNAs) are ubiquitous across the tree of life. Although tRNA structure is highly conserved, there is still significant variation in sequence features between clades, isotypes and even isodecoders. This variation not only impacts translation, but as shown by a variety of recent studies, nontranslation-associated functions are also sensitive to small changes in tRNA sequence. Despite the rapidly growing number of sequenced genomes, there is a lack of tools for both small- and large-scale comparative genomics analysis of tRNA sequence features. Here, we have integrated over 150\u00a0000 tRNAs spanning all domains of life into tRNAviz, a web application for exploring and visualizing tRNA sequence features. tRNAviz implements a framework for determining consensus sequence features and can generate sequence feature distributions by isotypes, clades and anticodons, among other tRNA properties such as score. All visualizations are interactive and exportable. The web server is publicly available at http:\/\/trna.ucsc.edu\/tRNAviz\/.<\/jats:p>","DOI":"10.1093\/nar\/gkz438","type":"journal-article","created":{"date-parts":[[2019,5,23]],"date-time":"2019-05-23T15:33:26Z","timestamp":1558625606000},"page":"W542-W547","source":"Crossref","is-referenced-by-count":34,"title":["tRNAviz: explore and visualize tRNA sequence features"],"prefix":"10.1093","volume":"47","author":[{"given":"Brian Y","family":"Lin","sequence":"first","affiliation":[{"name":"Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0810-1642","authenticated-orcid":false,"given":"Patricia P","family":"Chan","sequence":"additional","affiliation":[{"name":"Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3253-6021","authenticated-orcid":false,"given":"Todd M","family":"Lowe","sequence":"additional","affiliation":[{"name":"Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,5,25]]},"reference":[{"key":"2019062808324063700_B1","doi-asserted-by":"crossref","first-page":"171","DOI":"10.3389\/fgene.2014.00171","article-title":"tRNAs as regulators of biological processes","volume":"5","author":"Raina","year":"2014","journal-title":"Front. Genet."},{"key":"2019062808324063700_B2","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/nrm.2017.77","article-title":"The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis","volume":"19","author":"Schimmel","year":"2018","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2019062808324063700_B3","doi-asserted-by":"crossref","first-page":"4297","DOI":"10.1016\/j.febslet.2014.09.001","article-title":"tRNA fragments in human health and disease","volume":"588","author":"Anderson","year":"2014","journal-title":"FEBS Lett."},{"key":"2019062808324063700_B4","doi-asserted-by":"crossref","first-page":"6137","DOI":"10.1093\/nar\/gkl725","article-title":"Diversity of tRNA genes in eukaryotes","volume":"34","author":"Goodenbour","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2019062808324063700_B5","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1017\/S1355838202022021","article-title":"tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features","volume":"8","author":"Marck","year":"2002","journal-title":"RNA"},{"key":"2019062808324063700_B6","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1080\/15216540701604632","article-title":"Comparative RNomics and modomics in Mollicutes: prediction of gene function and evolutionary implications","volume":"59","author":"de\u00a0Crecy-Lagard","year":"2007","journal-title":"IUBMB Life"},{"key":"2019062808324063700_B7","doi-asserted-by":"crossref","first-page":"5017","DOI":"10.1093\/nar\/26.22.5017","article-title":"Universal rules and idiosyncratic features in tRNA identity","volume":"26","author":"Giege","year":"1998","journal-title":"Nucleic Acids Res."},{"key":"2019062808324063700_B8","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1016\/j.jmb.2009.12.018","article-title":"Functional analysis of human tRNA isodecoders","volume":"396","author":"Geslain","year":"2010","journal-title":"J. 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