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Computational Prediction of RNA–RNA Interactions

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RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1097))

Abstract

We describe different tools and approaches for RNA–RNA interaction prediction. Recognition of ncRNA targets is predominantly governed by two principles, namely the stability of the duplex between the two interacting RNAs and the internal structure of both mRNA and ncRNA. Thus, approaches can be distinguished into different major categories depending on how they consider inter- and intramolecular structure. The first class completely neglects the internal structure and measures only the stability of the duplex. The second class of approaches abstracts from specific intramolecular structures and uses an ensemble-based approach to calculate the effect of internal structure on a putative binding site, thus measuring the accessibility of the binding sites.

Since accessibility-based approaches can handle only one continuous interaction site, two addition types of approaches were introduced which predict a joint structure for the interacting RNAs. Since this problem is NP-complete, the approaches can handle only a restricted class of joint structures. The first are co-folding approaches, which predict a joint structure that is nested when the both sequences are concatenated. The last and most complex class of approaches impose only the restriction that they discard zipper-like structures. Finally, we will discuss the use of conservation information in RNA-target prediction.

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Notes

  1. 1.

    The precise definition of NP-complete is more complex. NP is a class of problems, which are currently believed to be different from the class P of problems that can be solved in polynomial time. Unless NP = P (which is believed to be very unlikely), there cannot be an algorithm that exactly solves the general interaction problem in polynomial time for all instances. However, there might be algorithms that solve the problem in reasonable time for most practical instances.

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Author information

Authors and Affiliations

  1. Lehrstuhl fur Bioinformatik, Albert-Ludwigs-Universitat, Freiburg, Germany

    Rolf Backofen

  2. Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark

    Rolf Backofen

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  1. Rolf Backofen
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Editors and Affiliations

  1. Center for non-coding RNA in Technology and Health, IKVH University of Copenhagen, Frederiksberg, Denmark

    Jan Gorodkin

  2. University of Washington Dept. Computer Science & Engineering, Seattle, Washington, USA

    Walter L. Ruzzo

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Backofen, R. (2014). Computational Prediction of RNA–RNA Interactions. In: Gorodkin, J., Ruzzo, W. (eds) RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Methods in Molecular Biology, vol 1097. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-709-9_19

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  • DOI: https://doi.org/10.1007/978-1-62703-709-9_19

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-708-2

  • Online ISBN: 978-1-62703-709-9

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