1. SHAPE directed RNA folding.
- Author
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Lorenz, Ronny, Luntzer, Dominik, Hofacker, Ivo L., Stadler, Peter F., and Wolfinger, Michael T.
- Subjects
- *
NUCLEOTIDES , *RNA , *THERMODYNAMICS , *ALGORITHMS , *PSEUDOCODE (Computer program language) - Abstract
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. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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