title: Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  BACKGROUND
  pkerp@tbi.univie.ac.at
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Währinger Straße 17/3, A-1090 Vienna, Austria and.
authors.forename: Peter
authors.initials: P
authors.lastname: Kerpedjiev
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Währinger Straße 17/3, A-1090 Vienna, Austria and Research Group Bioinformatics and Computational Biology, University of Vienna, Währinger Straße 29, A-1090 Vienna, Austria.
authors.forename: Stefan
authors.initials: S
authors.lastname: Hammer
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Währinger Straße 17/3, A-1090 Vienna, Austria and Research Group Bioinformatics and Computational Biology, University of Vienna, Währinger Straße 29, A-1090 Vienna, Austria.
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
mesh_terms: D020029:Base Pairing; D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012984:Software
chemical_list: D012313:RNA