SHAPE directed RNA folding.
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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.atSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Lorenz R
PROVIDER: S-EPMC4681990 | biostudies-literature |
REPOSITORIES: biostudies-literature
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