Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams

By Peter Kerpedjiev, S. Hammer, Ivo L. Hofacker. Bioinform., 2015

506 citations recorded by the source corpus.

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. 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. 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. Contact: pkerp@tbi.univie.ac.at Supplementary information: Supplementary data are available at Bioinformatics online.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b84cf641f05f5eff912beb175737309460323971

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Citations in the corpus

RNAcentral: a hub of information for non-coding RNA sequences (2018, background): “RNAcentral also displays RNA secondary structures provided by GtRNAdb using Forna (22) (Figure 3).”
3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction (2019, background): “Figure 4a shows the complicated 2D structure of 4ADV plotted by Forna [36], and Figure 4b shows the predicted and native 3D structure of it.”
NONCODEV5: a comprehensive annotation database for long non-coding RNAs (2017, methodology): “The RNA secondary structure of each transcript can be accessed through the NONCODE website; this option is supported by the RNA secondary structure visualization tool forna (67), which allows RNA secondary structures to be displayed directly in the browser (Figure 2).”