Publikationsdatum:
2015-12-18
Beschreibung:
: 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.
Print ISSN:
1367-4803
Digitale ISSN:
1460-2059
Thema:
Biologie
,
Informatik
,
Medizin
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