Jennifer, here’s how I get pairing probabilities from Vienna.

The basic idea is to get Vienna RNA’s RNAfold to create a PDF file for the dot plot and then examine the PDF file as a text file. If you are only looking at a few PDF files, requesting them from the Web server is probably easiest. But if you want to process a large batch of them, it is probably best to download the ViennaRNA package to your own machine and generate the PDF files locally.

To get the dot plot PDF from the, Web server, cut and paste your sequence into the first box. Make sure the “minimum free energy (MFE) and partition function” option is selected, and click on Proceed.

You’ll get a page saying your job has been submitted to the queue. Typically, in 10-20 seconds, this will be replaced by a screen showing you the results.

Find the line that says “You may look at the dot plot containing the base plot probabilities” and click on the PDF option. You should get something like this:

Although formatted slightly differently, this is essentially the same dot plot you see in the game UI. The biggest difference is that the probability vales are indicated by the area of the dot, rather than by a gray scale level.

To extract the numeric values for the probabilities, copy the PDF file to your local drive and open the file with a text editor.

Whoops! I just discovered that the PDF file generated on the server has the drawing data in a compressed format. This isn’t what happens when I produce the files locally. But, it turns out that the EPS file generated on the server works, so download that instead and open it with a text editor. Now scroll down to the line “%start of base pair probability data”.

Each of these lines describes one dot in the dot plot. The first line, “1 27 0.013068432 ubox” says that the box (“dot”) in the upper (right) half of the graph, at the intersection of row 1 and column 27, should have a side of 0.013068432 units wide. Since the area of a square box is equal to the square of its sides, the box will have an area of 0.00017078391494 square units. This means that the probability of finding base pairs 1 and 27 paired at any point in time is 0.00017078391494, or 0.017%.

But I suspect what you really want, if you’re going to methodically processes the results, is to is to download the ViennaLib software and script the whole process. But then, the details of the process are going to depend on your environment and preferred scripting language(s). I’m currently using a Mac, so I needed to build the software locally, and then used a combination of shell scripting, python and manual operations to semi-automate the extraction of the specific data I was interested in. If you are going to go this route, I’l be happy to share what I’ve done in more detail.

Hope this helps.