RNA-DV provides an interactive GUI toolkit for visualizing and designing RNA secondary structures. It allows users to interact directly with the RNA 2-d planar structure and modify it by altering primary sequence content and connect/disconnect nucleotide bonds. It integrates thermodynamic energy calculations including

  • efn2
  • HotKnots
  • Major
  • RNAeval

It also recognizes a number of secondary structure formats including CT, RNAML and dot bracket (dp). For details, please look at the following papers

  • Herbert H. Tsang and Denny C. Dai, “RNA-DV: an interactive tool for editing and visualizing RNA secondary structures”. BCB ’12 Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 2012 (link)

A user manual is here GUIManual. There is also a screencast demo


Source Code