Abstract
The prediction of RNA structure can be a first important step for the functional characterization of novel ncRNAs. Especially for the very meaningful secondary structure, there is a multitude of computational prediction tools. They differ not only in algorithmic details and the underlying models but also in what exactly they are trying to predict. This chapter gives an overview of different programs that aim to predict RNA secondary structure. We will introduce the ViennaRNA software package and web server as a solution that implements most of the varieties of RNA secondary structure prediction that have been published over the years. We focus on algorithms going beyond the mere prediction of a static structure.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Zuker, M., Stiegler, P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9, 133–148.
Eddy, S., Durbin, R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res 22, 2079–2088.
McCaskill, J. (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105–1119.
Do, C., Woods, D., Batzoglou, S. (2006) Contrafold: RNA secondary structure prediction without physics-based models. Bioinformatics 22, 90–98.
Sato, K., Hamada, M., Asai, K., Mituyama, T. (2009) Centroidfold: a web server for RNA secondary structure prediction. Nucleic Acids Res 37(Web Server issue), 277–2780.
Chan, C., Lawrence, C., Ding, Y. (2005) Structure clustering features on the sfold web server. Bioinformatics 21, 3926–3928.
Wuchty, S., Fontana, W., Hofacker, I., Schuster, P. (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49, 145–165.
Mathews, D., Sabina, J., Zuker, M., Turner, D. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288, 911–940.
Tafer, H., Ameres, S., Obernosterer, G., et al. (2008) The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol 26, 578–583.
Gruber, A., Lorenz, R., Bernhart, S., et al. (2008) The Vienna RNA websuite. Nucleic Acids Res 36(Web Server issue), 70–74.
Andronescu, M., Condon, A., Hoos, H., et al. (2007) Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics 23, 19–28.
Katoh, K., Kuma, K., Toh, H., Miyata, T. (2005) Mafft version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33, 511–518.
Larkin, M., Blackshields, G., Brown, N., et al. (2007) Clustal w and clustal x version 2.0. Bioinformatics 23, 2947–2948.
Markham, N., Zuker, M. (2008) Unafold: software for nucleic acid folding and hybridization. Methods Mol Biol 453, 3–31.
Mathews, D., Disney, M., Childs, J., et al. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA 101, 7287–7292.
Torarinsson, E., Lindgreen, S. (2008) War: web server for aligning structural RNAs. Nucleic Acids Res 36(Web Server issue), 79–84.
Flamm, C., Hofacker, I.L. (2008) Beyond energy minimization: approaches to the kinetic folding of RNA. Monatsh. f. Chemie 139, 447–457.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Bernhart, S.H. (2011). RNA Structure Prediction. In: Yu, B., Hinchcliffe, M. (eds) In Silico Tools for Gene Discovery. Methods in Molecular Biology, vol 760. Humana Press. https://doi.org/10.1007/978-1-61779-176-5_19
Download citation
DOI: https://doi.org/10.1007/978-1-61779-176-5_19
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-175-8
Online ISBN: 978-1-61779-176-5
eBook Packages: Springer Protocols