SHAPE directed RNA folding
Copyright policy )SHAPE directed RNA folding
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.at Supplementary information: Supplementary data are available at Bioinformatics online.
- Max Planck Institute for Mathematics in the Sciences Germany
- University of Copenhagen Denmark
- Universität Wien Austria
- University of copenhaguen Denmark
- University of Copenhagen Denmark
RNA Folding, SECONDARY STRUCTURE, Base Sequence, PREDICTION, Molecular Sequence Data, CONSTRAINTS, Applications Notes, 106005 Bioinformatik, RNA, Ribosomal, Escherichia coli, Nucleic Acid Conformation, Thermodynamics, 106005 Bioinformatics, Algorithms
RNA Folding, SECONDARY STRUCTURE, Base Sequence, PREDICTION, Molecular Sequence Data, CONSTRAINTS, Applications Notes, 106005 Bioinformatik, RNA, Ribosomal, Escherichia coli, Nucleic Acid Conformation, Thermodynamics, 106005 Bioinformatics, Algorithms
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