SHAPE directed RNA folding

Summary Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamics-based RNA secondary structure prediction algorithms can be implemented by means of soft constraints. This amounts to incorporating suitable pseudo-energies into the standard energy model for RNA secondary structures. As a showcase application for this new feature of the viennaRNA Package we compare three distinct, previously published strategies to utilize SHAPE reactivities for structure prediction. The new tool is benchmarked on a set of RNAs with known reference structure. Availability and implementation The capability for SHAPE directed RNA folding is part of the upcoming release of the viennaRNA Package 2.2 , for which a preliminary release is already freely available at http://www.tbi.univie.ac.at/RNA . Contact [email protected] Supplementary information Supplementary data is attached.