It's better to compare several software altogether in prediction of structure.

http://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software

Feyzollah is right, the complete list is there. RNAfold is easy and does what it says it does.

Yes, I have used RNAfold and its very simple to run and its quite fine

RNAstructure (http://rna.urmc.rochester.edu/RNAstructure.html) or mFold (http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form) are two good software systems that you can start with. However, I agree with what Feyzollah said, compare predictions generated by various programs. Also, keep in mind that without any experimental data incorporated into RNA structure predictions on average you achieve ~70% accuracy.

Hi all, my question was not on a program for predicting 2D RNA structures, but to VISUALIZE them. I wan to input any structure either predicted by a method or experimentally determinat and visualize it.

Varna (http://varna.lri.fr/) or Pseudoviewer (http://pseudoviewer.inha.ac.kr/). The latter lets you to visualize pseudoknots. Both are pretty good. Varna allows you to include pseudo-energy constrains from shape (color each base the way you want)

To me mfold is pretty easy to use, you can try it.

http://mfold.rna.albany.edu/?q=mfold/download-mfold

Hi Toni,

You can use VARNA (http://varna.lri.fr/), a java based applet for visualization of RNA 2D structures, which is easy to use but can not perform RNA comparison.

You can also use XRNA (http://rna.ucsc.edu/rnacenter/xrna/xrna.html), one of the most comprehensive RNA visualization tools. It will take a while for you to understand before you start using it. I am not sure if this has a comparison module.

For comparison of two structures though, I have used jViz.RNA which is again a java based applet. It uses a spring model to draw RNA structures which is quite handy to manipulate, but becomes sloppy while working on bigger RNA structures because of the same reason. Unfortunately, the website looks down right now, so I think the best way to obtain the software is to contact the authors (http://www.ncbi.nlm.nih.gov/pubmed/16220684).

Hi,

The best visualizer is VARNA : http://varna.lri.fr/

Regards

Hi Toni and Piyush,

There are several ways to compare structures within VARNA.

The first and easiest one uses a matrix representation, described for instance in:

http://varna.lri.fr/index.php?lang=en&css=varna&page=tutorial9

This should fulfill every specified requirements (zoom/pan, export facilities both in PS and SVG), with the only limitation that you'll have to create two distinct SVG files, and merge them manually (eg within Inkscape).

Other ways rely on more "obscure options". For instance, if the "real" alignment between two secondary structures is known (e.g. from RFAM data, or if they represent alternative structures for a given sequences), the two structures can sometimes be merged and drawn as a "super secondary structure" (or consensus secondary structure, of RFAM fame) that somehow summarizes both structures within a single diagram.

http://varna.lri.fr/index.php?lang=en&page=tutorial15&css=varna

Another interactive way to represent similarity is to systematically superimpose both structures based on the mapping, so visually similar regions tend to have similar orientations. It is also implemented within VARNA, but I consider this mode as a rough sketch rather than a mature visualization, so please contact me if you feel this could be useful to you.

Finally, don't hesitate to contact me if you have something else on your mind, I am generally interested in having VARNA offer new visualizations to represent structure similarity.

Cheers,

Yann

Hello, a good program is 4SALE; it uses sequence-structure data in dot-bracket format, you could create/modify the secondary structure of your sequences and you could do an aligment of the sequences by considering also their secondary structure. The best part is that the program has a viewer in which you could see the structure of single or multiple selected sequences; if you modify the structure, it is inmediately shown in the viewer. It is written in Java so it is multiplatform. You could find it in:

http://4sale.bioapps.biozentrum.uni-wuerzburg.de/

The program has some drawbacks, as it freezes from time to time (mainly with the viewer), or the viewer may stop refreshing the image (i.e., after changing the structure) so you have to close it and then re-open (and the program doesn't notice you about unsaved data). Despite this, I recommend it. Hope it helps.

if your input format is CT, you can use the following softs: jViz.RNA, PseudoViewer, S2S and VARNA. Depending on the data and the representation, some of the 4 softs may be more relevant: PseudoViewer if your structures include pseudo-knots, jViz.RNA for circular, linear or graph representations, VARNA if you want to add some annotations, S2S if you have structural data (3D or information on tertiary interactions).

I know this is an old thread, but I came across this question first, then found this recent (2016) review of RNA visualisation tools very useful: Article RNA Visualization: Relevance and the Current State-of-the-Ar...

We have developed RNAStructViz at Georgia Tech to assist with comparisons of RNA secondary structures: https://github.com/gtDMMB/RNAStructViz. It also has a built-in CT file viewer and provides conversions from CT format to other standard text-based formats. The package is easy to install as a Brew tap on Mac OS. See the user documentation at https://github.com/gtDMMB/RNAStructViz/wiki.