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 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 2.2, for which a preliminary release is already freely available at http://www.tbi.univie.ac.at/RNA.Contact: michael.wolfinger@univie.ac.atSupplementary information: Supplementary data are available at Bioinformatics online.

Summary:Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamicsbased 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.