RNAalifold analyses the pattern of base pair conservation in an RNA alignment in order to predict a consensus secondary structure.
It is part of the Vienna RNA Secondary Structure Prediction and Comparison Package. It was described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, and Peter F. Stadler, RNAalifold: Improved consensus structure prediction for RNA alignments (BMC Bioinformatics, 9:474, 2008). Download the paper at http://www.biomedcentral.com/1471-2105/9/474.

Running RNAalifold from Jalview

Jalview supports access to RNAalifold services provided by JABA 2.1 servers. To enable RNAalifold predictions for an RNA alignment, go to Webservices→Secondary Structure Prediction and select RNAalifold prediction to run with current defaults, and Change settings ... to adjust prediction parameters. The RNA secondary structure prediction for the alignment will be shown as alignment annotation, and any edits will trigger the prediction to be recalculated.

RNAalifold prediction parameters
JABAWS and Jalview only provide access to a selection of the RNAalifold arguments. For a full description, see the documentation at http://www.tbi.univie.ac.at/RNA/RNAalifold.html.

Supported Arguments which give alternate structures

Partition Function (-p)
Calculate the Partition Function and base pairing probability matrix in addition to the mfe structure. A coarse representation of the pair probabilities in the form of a pseudo bracket notation, as well as the centroid structure derived from the pair probabilities are displayed. The most likely base pairings are stored in a separate file by RNAalifold and represented in Jalview by a bar graph annotation line labeled 'Contact Probabilities'.

Maximum Expected Accuracy Structure (--MEA)
Calculate an MEA structure where the expected Accuracy is computed from the base pair probabilities. A more detailed description can be found in the RNAfold program documentation at http://www.tbi.univie.ac.at/RNA/RNAfold.html.

Example RNAalifold Structure Annotation rows