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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 ViennaRNA Package 2.2, for which a preliminary release is already freely available at http://www.tbi.univie.ac.at/RNA.

Contact

michael.wolfinger@univie.ac.at

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Lorenz R 

PROVIDER: S-EPMC4681990 | biostudies-literature |

REPOSITORIES: biostudies-literature

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