SHAPE directed RNA folding.
CONCLUSIONS
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.


METHODS
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.


BACKGROUND
michael.wolfinger@univie.ac.at


BACKGROUND
Supplementary data are available at Bioinformatics online.
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria, Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.
Ronny
R
Lorenz
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.
Dominik
D
Luntzer
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria, Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.
Ivo L
IL
Hofacker
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria, Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.
Peter F
PF
Stadler
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria, Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.
Michael T
MT
Wolfinger
D000465:Algorithms; D001483:Base Sequence; D004926:Escherichia coli / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D059370:RNA Folding; D012335:RNA, Ribosomal / Q000235:genetics; D013816:Thermodynamics
D012335:RNA, Ribosomal