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Updated: Jun 17, 2026
13:42
RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
Faster computation of exact RNA shape probabilities
Stefan Janssen1, Robert Giegerich
1Practical Computer Science, Faculty of Technology, Bielefeld University, D-33615 Bielefeld, Germany.
Bioinformatics (Oxford, England)
|January 19, 2010
Summary
RapidShapes significantly accelerates RNA shape probability calculations by focusing on high-probability structures. This method offers substantial speed-ups, making advanced RNA analysis feasible for larger datasets.
Area of Science:
- Computational Biology
- Bioinformatics
- Structural Biology
Background:
- Abstract shape analysis provides insights into RNA folding.
- Shape probabilities offer sequence-independent information superior to free energies.
- Previous methods for shape probability computation were computationally expensive, scaling exponentially with sequence length.
Purpose of the Study:
- To develop a faster method for computing RNA shape probabilities.
- To enable probabilistic shape analysis for medium-scale applications.
Main Methods:
- Introduced RapidShapes, an approach to compute shapes above a probability threshold.
- Generates a list of promising shapes and specialized folding programs.
- Computes the Boltzmann probability share for each selected shape.
Main Results:
- RapidShapes achieves a 10-138 fold speed-up for RNA sequences of length 400.
- Only a small fraction of shapes require explicit computation.
- The method maintains exact probability values.
Conclusions:
- RapidShapes makes probabilistic RNA shape analysis computationally feasible.
- This advancement supports applications like screening RNA transcripts in bacterial genomes.
- The software is available at http://bibiserv.cebitec.uni-bielefeld.de/rnashapes.
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