Abstract
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.atSupplementary information: Supplementary data are available at Bioinformatics online.
Highlights
The use of secondary structure diagrams is ubiquitous within the field of RNA biology
Integrated Structure Prediction (Supplementary Material Section 1.1.5): To simplify the process of going from sequence to secondary structure, forna provides a transparent interface to the Vienna RNA Package (Lorenz et al, 2011) which automatically calculates the minimum free energy for a particular sequence if no secondary structure is provided
Reusable Display Container (Supplementary Material Section 1.2): Researchers can effortlessly share RNA structures online by adding a few lines of javascript to their web page and showing a diagram of the secondary structure embedded as an SVG container attached to any specified element in the DOM tree
Summary
The use of secondary structure diagrams is ubiquitous within the field of RNA biology. The contents and positions of sub-structures such as hairpin loops, interior loops, multiloop junctions and external loops are immediately evident. Such information is of great value to researchers seeking to identify putative mutations to perform when seeking to isolate the structural basis of a biological effect, to find protein binding, and to provide a context for observed behaviour. It is used as both an exploratory as well as a communicative tool. For visualizing the secondary structure of RNA molecules, with the exception of PseudoViewer, none are available online without java and none offer the flexibility in exploring, arranging and manipulating the structure that forna does (See Table 1 for an enumerated comparison of features)
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