ArticleBioinformatics (Oxford, England)2010
Faster computation of exact RNA shape probabilities.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Classified Dynamic Programming in RNA Structure Analysis.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Insertions and deletions in the RNA sequence-structure map.Journal of the Royal Society, Interface · 2021Article
- Article
- Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.BMC bioinformatics · 2018Article
- Thermodynamic matchers for the construction of the cuckoo RNA family.RNA biology · 2015Article
- Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment.GigaScience · 2014Article
- Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM.BMC bioinformatics · 2013Article
- BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms.Advances in bioinformatics · 2012Article
- Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction.BMC bioinformatics · 2011Article
- Selective translational control of the Alzheimer amyloid precursor protein transcript by iron regulatory protein-1.The Journal of biological chemistry · 2010Article
- TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.PLoS computational biology · 2010Article
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2 authors.
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Abstract
motivationAbstract shape analysis allows efficient computation of a representative sample of low-energy foldings of an RNA molecule. More comprehensive information is obtained by computing shape probabilities, accumulating the Boltzmann probabilities of all structures within each abstract shape. Such information is superior to free energies because it is independent of sequence length and base composition. However, up to this point, computation of shape probabilities evaluates all shapes simultaneously and comes with a computation cost which is exponential in the length of the sequence.
resultsWe device an approach called RapidShapes that computes the shapes above a specified probability threshold T by generating a list of promising shapes and constructing specialized folding programs for each shape to compute its share of Boltzmann probability. This aims at a heuristic improvement of runtime, while still computing exact probability values.
conclusionEvaluating this approach and several substrategies, we find that only a small proportion of shapes have to be actually computed. For an RNA sequence of length 400, this leads, depending on the threshold, to a 10-138 fold speed-up compared with the previous complete method. Thus, probabilistic shape analysis has become feasible in medium-scale applications, such as the screening of RNA transcripts in a bacterial genome. AVAILABILITY: RapidShapes is available via http://bibiserv.cebitec.uni-bielefeld.de/rnashapes
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