SHAPE directed RNA folding.

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

SUBMITTER: Lorenz R 

PROVIDER: S-EPMC4681990 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature