{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,5]],"date-time":"2026-04-05T09:07:48Z","timestamp":1775380068790,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,11,3]],"date-time":"2016-11-03T00:00:00Z","timestamp":1478131200000},"content-version":"vor","delay-in-days":764,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation : Abstract shape analysis, first proposed in 2004, allows one to extract several relevant structures from the folding space of an RNA sequence, preferable to focusing in a single structure of minimal free energy. We report recent extensions to this approach.<\/jats:p>\n               <jats:p>Results : We have rebuilt the original RNA shapes as a repository of components that allows us to integrate several established tools for RNA structure analysis: RNA shapes , RNA alishapes and pknots RG, including its recent extension p K iss . As a spin-off, we obtain heretofore unavailable functionality: e. g. with p K iss , we can now perform abstract shape analysis for structures holding pseudoknots up to the complexity of kissing hairpin motifs. The new tool p A li K iss can predict kissing hairpin motifs from aligned sequences. Along with the integration, the functionality of the tools was also extended in manifold ways.<\/jats:p>\n               <jats:p>Availability and implementation : As before, the tool is available on the Bielefeld Bioinformatics server at http:\/\/bibiserv.cebitec.uni-bielefeld.de\/rnashapesstudio .<\/jats:p>\n               <jats:p>Contact : bibi-help@cebitec.uni-bielefeld.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu649","type":"journal-article","created":{"date-parts":[[2014,10,2]],"date-time":"2014-10-02T06:07:10Z","timestamp":1412230030000},"page":"423-425","source":"Crossref","is-referenced-by-count":140,"title":["The RNA shapes studio"],"prefix":"10.1093","volume":"31","author":[{"given":"Stefan","family":"Janssen","sequence":"first","affiliation":[{"name":"Practical Computer Science, Faculty of Technology, Bielefeld University, D-33615 Bielefeld, Germany"}]},{"given":"Robert","family":"Giegerich","sequence":"additional","affiliation":[{"name":"Practical Computer Science, Faculty of Technology, Bielefeld University, D-33615 Bielefeld, Germany"}]}],"member":"286","published-online":{"date-parts":[[2014,10,1]]},"reference":[{"key":"2023020116164038900_btu649-B1","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1016\/j.virol.2004.11.038","article-title":"Programmed ribosomal frameshifting in decoding the sars-cov genome","volume":"332","author":"Baranov","year":"2005","journal-title":"Virology"},{"key":"2023020116164038900_btu649-B2","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1186\/1471-2105-9-474","article-title":"RNAalifold: improved consensus structure prediction for RNA alignments","volume":"9","author":"Bernhart","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023020116164038900_btu649-B3","doi-asserted-by":"crossref","first-page":"D226","DOI":"10.1093\/nar\/gks1005","article-title":"Rfam 11.0: 10 years of RNA families","volume":"41","author":"Burge","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023020116164038900_btu649-B4","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":"2023020116164038900_btu649-B5","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/j.scico.2003.12.005","article-title":"A discipline of dynamic programming over sequence data","volume":"51","author":"Giegerich","year":"2004","journal-title":"Sci. Comput. Program."},{"key":"2023020116164038900_btu649-B6","doi-asserted-by":"crossref","first-page":"4843","DOI":"10.1093\/nar\/gkh779","article-title":"Abstract shapes of RNA","volume":"32","author":"Giegerich","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023020116164038900_btu649-B7","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1186\/1471-2105-12-429","article-title":"Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction","volume":"12","author":"Janssen","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023020116164038900_btu649-B8","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. 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