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