PT  - JOURNAL ARTICLE
AU  - Dominik Luntzer
AU  - Ronny Lorenz
AU  - Ivo L. Hofacker
AU  - Peter F. Stadler
AU  - Michael T. Wolfinger
TI  - SHAPE directed RNA folding
AID  - 10.1101/015537
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 015537
4099  - http://biorxiv.org/content/early/2015/02/20/015537.short
4100  - http://biorxiv.org/content/early/2015/02/20/015537.full
AB  - 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 michael.wolfinger{at}univie.ac.atSupplementary information Supplementary data is attached.