SHAPE directed RNA folding
Open Access
- 9 September 2015
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 32 (1) , 145-147
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.Keywords
All Related Versions
This publication has 10 references indexed in Scilit:
- Forna (force-directed RNA): Simple and effective online RNA secondary structure diagramsBioinformatics, 2015
- Insights into RNA structure and function from genome-wide studiesNature Reviews Genetics, 2014
- Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and GenomesAnnual Review of Biophysics, 2014
- Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknotsProceedings of the National Academy of Sciences, 2013
- Integrating Chemical Footprinting Data into RNA Secondary Structure PredictionPLOS ONE, 2012
- RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure predictionNucleic Acids Research, 2012
- ViennaRNA Package 2.0Algorithms for Molecular Biology, 2011
- Accurate SHAPE-directed RNA structure determinationProceedings of the National Academy of Sciences, 2009
- The Vienna RNA WebsuiteNucleic Acids Research, 2008
- Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structureProceedings of the National Academy of Sciences, 2004