ArticleBMC biology2006
Complete probabilistic analysis of RNA shapes.
Article in BMC biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 80 citations in OpenAlex.
- Classified Dynamic Programming in RNA Structure Analysis.Methods in molecular biology (Clifton, N.J.) · 2024Article
- The non-deterministic genotype-phenotype map of RNA secondary structure.Journal of the Royal Society, Interface · 2023Article
- Fast free-energy-based neutral set size estimates for the RNA genotype-phenotype map.Journal of the Royal Society, Interface · 2022Article
- Insertions and deletions in the RNA sequence-structure map.Journal of the Royal Society, Interface · 2021Article
- Simulation of Folding Kinetics for Aligned RNAs.Genes · 2021Article
- Towards an understanding of RNA structural modalities: a riboswitch case study.Computational and mathematical biophysics · 2019Article
- Article
- Compound image segmentation of published biomedical figures.Bioinformatics (Oxford, England) · 2018Article
- RNArchitecture: a database and a classification system of RNA families, with a focus on structural information.Nucleic acids research · 2018Article
- The BRaliBase dent-a tale of benchmark design and interpretation.Briefings in bioinformatics · 2017Article
- Computational prediction of regulatory, premature transcription termination in bacteria.Nucleic acids research · 2017Article
- New insights from cluster analysis methods for RNA secondary structure prediction.Wiley interdisciplinary reviews. RNA · 2016Review
- The RNA shapes studio.Bioinformatics (Oxford, England) · 2015Article
- Algebraic Dynamic Programming over general data structures.BMC bioinformatics · 2015Article
- Pareto optimization in algebraic dynamic programming.Algorithms for molecular biology : AMB · 2015Article
- Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble.Nucleic acids research · 2014Article
- Combinatorics of locally optimal RNA secondary structures.Journal of mathematical biology · 2014Article
- A silent exonic SNP in kdm3a affects nucleic acids structure but does not regulate experimental autoimmune encephalomyelitis.PloS one · 2013Article
- Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM.BMC bioinformatics · 2013Article
- Abstract folding space analysis based on helices.RNA (New York, N.Y.) · 2012Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSoon after the first algorithms for RNA folding became available, it was recognised that the prediction of only one energetically optimal structure is insufficient to achieve reliable results. An in-depth analysis of the folding space as a whole appeared necessary to deduce the structural properties of a given RNA molecule reliably. Folding space analysis comprises various methods such as suboptimal folding, computation of base pair probabilities, sampling procedures and abstract shape analysis. Common to many approaches is the idea of partitioning the folding space into classes of structures, for which certain properties can be derived.
resultsIn this paper we extend the approach of abstract shape analysis. We show how to compute the accumulated probabilities of all structures that share the same shape. While this implies a complete (non-heuristic) analysis of the folding space, the computational effort depends only on the size of the shape space, which is much smaller. This approach has been integrated into the tool RNA shapes, and we apply it to various RNAs.
conclusionAnalyses of conformational switches show the existence of two shapes with probabilities approximately 2/3 vs. 1/3, whereas the analysis of a microRNA precursor reveals one shape with a probability near to 1.0. Furthermore, it is shown that a shape can outperform an energetically more favourable one by achieving a higher probability. From these results, and the fact that we use a complete and exact analysis of the folding space, we conclude that this approach opens up new and promising routes for investigating and understanding RNA secondary structure.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.