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Media type:
E-Article
Title:
The RNA shapes studio
Contributor:
Janssen, Stefan;
Giegerich, Robert
Published:
Oxford University Press (OUP), 2015
Published in:
Bioinformatics, 31 (2015) 3, Seite 423-425
Language:
English
DOI:
10.1093/bioinformatics/btu649
ISSN:
1367-4811;
1367-4803
Origination:
Footnote:
Description:
Abstract 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. 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. Availability and implementation : As before, the tool is available on the Bielefeld Bioinformatics server at http://bibiserv.cebitec.uni-bielefeld.de/rnashapesstudio . Contact : bibi-help@cebitec.uni-bielefeld.de