{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T16:37:40Z","timestamp":1732034260227},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: TRFolder-W is a web server capable of predicting core structures of telomerase RNA (TR) in yeast genomes. TRFolder is a command-line Python toolkit for TR-specific structure prediction. We developed a web-version built on the django web framework, leveraging the work done previously, to include enhancements to increase flexibility of usage. To date, there are five core sub-structures commonly found in TR of fungal species, which are the template region, downstream pseudoknot, boundary element, core-closing stem and triple helix. The aim of TRFolder-W is to use the five core structures as fundamental units to predict potential TR genes for yeast, and to provide a user-friendly interface. Moreover, the application of TRFolder-W can be extended to predict the characteristic structure on species other than fungal species.<\/jats:p>\n               <jats:p>Availability: The web server TRFolder-W is available at http:\/\/rna-informatics.uga.edu\/?f=software&amp;p=TRFolder-w.<\/jats:p>\n               <jats:p>Contact: cai@cs.uga.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0http:\/\/rna-informatics.uga.edu\/?f=software&amp;p=TRFolder-w-supplement.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts506","type":"journal-article","created":{"date-parts":[[2012,8,25]],"date-time":"2012-08-25T02:27:06Z","timestamp":1345861626000},"page":"2696-2697","source":"Crossref","is-referenced-by-count":2,"title":["TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes"],"prefix":"10.1093","volume":"28","author":[{"given":"Dong","family":"Zhang","sequence":"first","affiliation":[{"name":"1 Institute of Bioinformatics and 2Department of Computer Science and 3Department of Plant Biology, University of Georgia, Athens, GA 30602, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xingran","family":"Xue","sequence":"additional","affiliation":[{"name":"1 Institute of Bioinformatics and 2Department of Computer Science and 3Department of Plant Biology, University of Georgia, Athens, GA 30602, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Russell L.","family":"Malmberg","sequence":"additional","affiliation":[{"name":"1 Institute of Bioinformatics and 2Department of Computer Science and 3Department of Plant Biology, University of Georgia, Athens, GA 30602, USA"},{"name":"1 Institute of Bioinformatics and 2Department of Computer Science and 3Department of Plant Biology, University of Georgia, Athens, GA 30602, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liming","family":"Cai","sequence":"additional","affiliation":[{"name":"1 Institute of Bioinformatics and 2Department of Computer Science and 3Department of Plant Biology, University of Georgia, Athens, GA 30602, USA"},{"name":"1 Institute of Bioinformatics and 2Department of Computer Science and 3Department of Plant Biology, University of Georgia, Athens, GA 30602, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,8,24]]},"reference":[{"key":"2023012513151964600_bts506-B1","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1261\/rna.1194009","article-title":"Identification and comparative analysis of telomerase RNAs from Candida species reveal conservation of functional elements","volume":"15","author":"Gunisova","year":"2009","journal-title":"RNA"},{"key":"2023012513151964600_bts506-B2","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1504\/IJBRA.2011.039170","article-title":"TRFolder: computational prediction of novel telomerase RNA structures in yeast genomes","volume":"7","author":"Guo","year":"2011","journal-title":"Int. J. Bioinform. Res. Appl."},{"key":"2023012513151964600_bts506-B3","doi-asserted-by":"crossref","first-page":"3605","DOI":"10.1016\/j.febslet.2009.10.034","article-title":"Large telomerase RNA, telomere length heterogeneity and escape from senescence in Candida glabrata","volume":"583","author":"Kachouri-Lafond","year":"2009","journal-title":"FEBS Lett"},{"key":"2023012513151964600_bts506-B4","doi-asserted-by":"crossref","first-page":"14713","DOI":"10.1073\/pnas.0405879101","article-title":"A universal telomerase RNA core structure includes structured motifs required for binding the telomerase reverse transcriptase protein","volume":"101","author":"Lin","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA."},{"key":"2023012513151964600_bts506-B5","doi-asserted-by":"crossref","first-page":"2130","DOI":"10.1128\/MCB.01826-06","article-title":"A triple helix within a pseudoknot is a conserved and essential element of telomerase RNA","volume":"27","author":"Shefer","year":"2007","journal-title":"Mol. Cell. Biol."},{"key":"2023012513151964600_bts506-B6","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1126\/science.288.5467.863","article-title":"Template boundary in a yeast telomerase specified by RNA structure","volume":"288","author":"Tzfati","year":"2000","journal-title":"Science"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/20\/2696\/48874504\/bioinformatics_28_20_2696.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/20\/2696\/48874504\/bioinformatics_28_20_2696.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T19:19:01Z","timestamp":1674674341000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/20\/2696\/207418"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,8,24]]},"references-count":6,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2012,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts506","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,10,15]]},"published":{"date-parts":[[2012,8,24]]}}}