SHAPE directed RNA folding with the ViennaRNA Package
The ViennaRNA Package supports three published approaches for SHAPE-guided RNA structure prediction. Here we evaluate and compare the methods by Deigan, Zarringhalam, and Washietl
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 ViennaRNA 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 32: 145–47 (2016) | doi:10.1093/bioinformatics/btv523 | PDF