Journal
BIOINFORMATICS
Volume 32, Issue 1, Pages 145-147Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btv523
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Funding
- Austrian Science Fund (FWF) project 'RNA regulation of the transcriptome' [F43]
- Deutsche Forschungsgemeinschaft (DFG) [STA 850/15-1]
- German ministry of science (e:Bio initiative) [0316165C]
- Austrian/French project 'RNAlands' [FWF-I-1804N28, ANR-14-CE34-0011]
- Austrian Science Fund (FWF) [I1804] Funding Source: Austrian Science Fund (FWF)
- Agence Nationale de la Recherche (ANR) [ANR-14-CE34-0011] Funding Source: Agence Nationale de la Recherche (ANR)
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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.
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