{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T23:14:31Z","timestamp":1793142871529,"version":"4.5.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":468,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The secondary structure of RNA is integral to the variety of functions it carries out in the cell and its depiction allows researchers to develop hypotheses about which nucleotides and base pairs are functionally relevant. Current approaches to visualizing secondary structure provide an adequate platform for the conversion of static text-based representations to 2D images, but are limited in their offer of interactivity as well as their ability to display larger structures, multiple structures and pseudoknotted structures.<\/jats:p>\n               <jats:p>Results: In this article, we present forna, a web-based tool for displaying RNA secondary structure which allows users to easily convert sequences and secondary structures to clean, concise and customizable visualizations. It supports, among other features, the simultaneous visualization of multiple structures, the display of pseudoknotted structures, the interactive editing of the displayed structures, and the automatic generation of secondary structure diagrams from PDB files. It requires no software installation apart from a modern web browser.<\/jats:p>\n               <jats:p>Availability and implementation: The web interface of forna is available at http:\/\/rna.tbi.univie.ac.at\/forna while the source code is available on github at www.github.com\/pkerpedjiev\/forna.<\/jats:p>\n               <jats:p>Contact: \u00a0pkerp@tbi.univie.ac.at<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv372","type":"journal-article","created":{"date-parts":[[2015,6,23]],"date-time":"2015-06-23T00:20:09Z","timestamp":1435018809000},"page":"3377-3379","source":"Crossref","is-referenced-by-count":575,"title":["Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams"],"prefix":"10.1093","volume":"31","author":[{"given":"Peter","family":"Kerpedjiev","sequence":"first","affiliation":[{"name":"1 Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17\/3, A-1090 Vienna, Austria and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Hammer","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17\/3, A-1090 Vienna, Austria and"},{"name":"2 Research Group Bioinformatics and Computational Biology, University of Vienna, W\u00e4hringer Stra\u00dfe 29, A-1090 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivo L.","family":"Hofacker","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17\/3, A-1090 Vienna, Austria and"},{"name":"2 Research Group Bioinformatics and Computational Biology, University of Vienna, W\u00e4hringer Stra\u00dfe 29, A-1090 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,6,22]]},"reference":[{"key":"2023020202313769800_btv372-B1","first-page":"167","article-title":"An improved algorithm for nucleic acid secondary structure display","volume":"4","author":"Bruccoleri","year":"1988","journal-title":"Comput. Appl. Biosci."},{"key":"2023020202313769800_btv372-B2","doi-asserted-by":"crossref","first-page":"1435","DOI":"10.1093\/bioinformatics\/btp252","article-title":"PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots","volume":"25","author":"Byun","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020202313769800_btv372-B3","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1093\/bioinformatics\/btp250","article-title":"VARNA: interactive drawing and editing of the RNA secondary structure","volume":"25","author":"Darty","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020202313769800_btv372-B4","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1006\/jmbi.2001.4626","article-title":"Quantitative analysis of nucleic acid three-dimensional structures","volume":"308","author":"Gendron","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023020202313769800_btv372-B5","doi-asserted-by":"crossref","first-page":"2941","DOI":"10.1093\/bioinformatics\/btt496","article-title":"RNA secondary structure diagrams for very large molecules: RNAfdl","volume":"29","author":"Hecker","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020202313769800_btv372-B6","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/1748-7188-6-26","article-title":"ViennaRNA package 2.0","volume":"6","author":"Lorenz","year":"2011","journal-title":"Algorithms Mol. Biol."},{"key":"2023020202313769800_btv372-B7","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1109\/TNB.2005.853646","article-title":"jviz. rna-a java tool for RNA secondary structure visualization","volume":"4","author":"Wiese","year":"2005","journal-title":"IEEE Trans. Nanobioscience"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/20\/3377\/49035860\/bioinformatics_31_20_3377.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/20\/3377\/49035860\/bioinformatics_31_20_3377.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:50:15Z","timestamp":1675309815000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/20\/3377\/195918"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,6,22]]},"references-count":7,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2015,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv372","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,10,15]]},"published":{"date-parts":[[2015,6,22]]}}}