Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

Seemann, Stefan E.; Gorodkin, Jan; Backofen, Rolf

Hence, our approach is based on a combined MEA score. The combined score is based on both base pair and single-strand probabilities as calculated by RNAfold and the reliabilities of base pairs and single-stranded positions as extracted from Pfold. The combined MEA scoring has the advantage that it allows for an explicit weighting of the contribution of phylogenetic and thermodynamic information and smoothens the effects of incorrectly predicted base pair probabilities. The latter is due to the fact that the algorithm searches for a structure that shares as many base pairs as possible with all alternative structures. We implemented this Probabilistic Evolutionary and Thermodynamic folding algorithm (PETfold) for multiple RNA sequence alignments.