rna-dv
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
