If you want to predict the secondary structure – i.e. the basepairing interactions – for a single RNA sequence, you would normally rely on energy parameters and try to find the minimum free energy structure. If, however, you have multiple related sequences you suddenly have access to all the evolutionary information you get from a multiple alignment. This can be utilized.

The growing interest in non-coding RNAs in recent years has given rise to many different programs focused on aligning and predicting the secondary structure of ncRNAs. It can be difficult for a user to determine which one to use, to judge the different predictions, and sometimes even to run the programs. Therefore I and Stinus Lindgreen, implemented a webserver which provides users with an easy way to run the top methods available simultaneously, and get a combined, simple view of the predictions, which can be downloaded in various formats for further analysis. Additional measures are calculated for each program to make it easier to judge the individual predictions, and a consensus prediction taking all the programs into account is also calculated. The webserver will run globally and locally, where the local version simply uses CMfinder [Yao et al., 2006] to cut out the local regions that will then be fed to the other programs globally as usual.

The consensus is in itself a heatmap indicating how well the multiple alignment programs included agree on the prediction. This can be very valuable when studying unknown multiple sequences to find if they have well defined, reliable, sequence and structure conservation. Check out this example output.