Here we characterize a pseudoknot in the 5'UTR Internal Ribosome Entry Site (IRES) of Bovine Viral Diarrhea Virus (BVDV) using SHAPE-guided RNA structure probing and computational modelling of secondary and tertiary structures
This review explores methods for predicting RNA secondary structures by integrating reactivity information from experimental probing data. It highlights the limitations of traditional RNA structure prediction, which typically relies solely on thermodynamic models based on sequences
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