The RNA shapes studio

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

Cited by papers we hold 2

• RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning · 2019
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• A planarian nidovirus expands the limits of RNA genome size · 2018
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