One of the goals of this project is to embed a secondary structure viewer into Jalview for RNA. At today's meeting with Jim, it looks like there might be some interactive editing features that we'd like to implement into VARNA, if we choose it. Adding interactive base connection making and breaking would be nice. I'm pretty sure that we will use VARNA. The advantages of VARNA are:
1. It is written in Java and under the GPL license. This means that it can be easily added to Jalview.
2. You can specify secondary structure with WUSS notation
3. It exports the image you make in a variety of formats
4. (My opinion) It has pretty output.
5. You can add annotations and change color of bases
6. Other features allow different visualization schemes, such as basepairing and modes such as "Feynman's diagram"
7. Can handle a variety of file formats (.ct, .dbn, etc)
One interesting thing about VARNA is that it can create multiple panels in the visualization window. This might be useful for comparing a multiple sequence alignment. On the other hand, another type of visualization might be useful, such as overlaying the structures and using color to indicate conservation.
After looking at various RNA structure viewers, it looks like it might be useful to add more valid file formats in Jalview, such as ConnecT (.ct), Base Pair Sequence (.bpseq), and Dot Bracket Notation (.dbf, .dbn).
Below is a list of some RNA secondary structure viewers that I've looked at.
VARNA: Visualization Applet for RNA
List from: http://openwetware.org/wiki/Wikiomics:Alignment_visualization_and_plotting_RNA_structures