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RNA Secondary Structure Prediction by Minimum Free Energy

2006; Ogurtsov, Shabalina, Kondrashov, Roytberg

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Encyclopedia of Algorithms

Keywords and Synonyms

RNA Folding        

Problem Definition

This problem is concerned with predicting the set of base pairs formed in the native structure of an RNA molecule. The main motivation stems from structure being crucial for function and the growing appreciation of the importance of RNA molecules in biological processes. Base pairing is the single most important factor determining structure formation. Knowledge of the secondary structure alone also provides information about stretches of unpaired bases that are likely candidates for active sites. Early work [7] focused on finding structures maximizing the number of base pairs. With the work of Zuker and Stiegler [17] focus shifted to energy minimization in a model approximating the Gibbs free energy of structures.

Notation

Let \( { s \in \{A, C, G, U\}^* } \) denote the sequence of bases of an RNA molecule. Use \( { X \cdot Y } \) where \( { X, Y \in \{A, C, G, U\} } \) to denote a base pair between bases of type X and Y, and \( { i...

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Recommended Reading

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Author information

Authors and Affiliations

  1. Department of Statistics, Oxford University, Oxford, UK

    Rune B. Lyngsø

Authors
  1. Rune B. Lyngsø
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Editor information

Editors and Affiliations

  1. Department of Electrical Engineering and Computer ScienceMcCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA

    Ming-Yang Kao Professor of Computer Science

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Lyngsø, R. (2008). RNA Secondary Structure Prediction by Minimum Free Energy. In: Kao, MY. (eds) Encyclopedia of Algorithms. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-30162-4_347

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