With the advent of efficient strategies for experimental RNA structure validation, especially combination of chemical probing with next-generation sequencing technologies, came demand to couple experimental data, e.g. SHAPE reactivities, with in silico RNA structure prediction tools. In this line, the computational structure prediction is guided by in vitro or even in vivo probing data.

We have recently implemented three previously published methods for incorporation of SHAPE probing data into the Vienna RNA Package and benchmarked prediction results with a set of RNAs with known reference structures.

Don’t miss the Supplementary Data since it contains extensive coverage of the applied benchmark strategies and lots of background information.

SHAPE directed RNA folding
Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger
Bioinformatics 2015 btv523
DOI: 10.1093/bioinformatics/btv523

Abstract

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.