Abstract
RNA secondary structures can be predicted using efficient algorithms. A widely used software package implementing a large number of computational methods is the ViennaRNA Package. This chapter describes how to use programs from the ViennaRNA Package to perform common tasks such as prediction of minimum free-energy structures, suboptimal structures, or base pairing probabilities, and generating secondary structure plots with reliability annotation. Moreover, we present recent methods to assess the folding kinetics of an RNA via 2D projections of the energy landscape, identification of local minima and energy barriers, or simulation of RNA folding as a Markov process.
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Acknowledgements
This work was supported in part by the Austrian Science Foundation FWF project “SFB F43 RNA regulation of the transcriptome.”
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Hofacker, I.L., Lorenz, R. (2014). Predicting RNA Structure: Advances and Limitations. In: Waldsich, C. (eds) RNA Folding. Methods in Molecular Biology, vol 1086. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-667-2_1
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DOI: https://doi.org/10.1007/978-1-62703-667-2_1
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