RNApredator

The RNApredator (Eggenhofer et al., 2011) software facilitates the prediction of sRNA-mRNA interactions in bacteria. Currently targets can be searched in more than 1300 bacterial species. RNApredator uses a dynamic programming approach to compute putative targets. The main machinery used by RNApredator to find targets is the program called RNAplex. RNAplex is a new approach for RNA-RNA interaction search, which has a prediction accuracy similar to that of algorithms that explicitly consider intramolecular structures, but running at least three orders of magnitude faster than RNAup and IntaRNA. This is achieved by using a combination of pre-computed accessibility profiles, with an approximate energy- model, allowing to mimic the effects of the competition between intra- and intermolecular interactions.