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Thursday, May 20, 2010

RNA Secondary Structure Viewers

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


jViz.RNA 2.0






List from:


  1. Nice post. Does it make sense to modify the structure inside VARNA or inside Jalview and then regenerate the structure? Usually I'd do this in the context of an alignment since you'll only see a representative sequence (consensus, MIS, ...) inside VARNA.

  2. It would be nice to be able to modify the structure in both VARNA and Jalview and have the changes be reflected on either side, but I don't that will be feasible (at least in the time frame that I have to work on this project). I think that would make more sense to modify the structure within Jalview, then regenerate the structure in VARNA. Like you said, probably modifications to the structure will be done in the context of a multiple alignment, so you'd be using Jalview to do this. But, what would happen if you just want to play around with possible secondary structure of one sequence? Then it would be nice to have changes you make in VARNA be reflected in Jalview, especially in the context of the other features that I'm planning to implement (eg. highlighting regions that form stems with each other in the Jalview sequence window). Perhaps in that case an option to port changes back to the sequence window would be the way to do it, instead of making it automatic. We'll see what happens as I get to know VARNA and Jalview better...