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Encyclopedia of Algorithms pp 780–782Cite as

RNA Secondary Structure Prediction Including Pseudoknots

2004; Lyngsø

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Keywords and Synonyms

Abbreviated as Pseudoknot Prediction        

Problem Definition

This problem is concerned with predicting the set of base pairs formed in the native structure of an RNA molecule, including overlapping base pairs also known as pseudoknots. Standard approaches to RNA secondary structure prediction only allow sets of base pairs that are hierarchically nested. Though few known real structures require the removal of more than a small percentage of their base pairs to meet this criteria, a significant percentage of known real structures contain at least a few base pairs overlapping other base pairs. Pseudoknot substructures are known to be crucial for biological function in several contexts. One of the more complex known pseudoknot structures is illustrated in Fig. 1

Figure 1
figure 1

Secondary structure of the Escherichia coli α operon mRNA from position 16 to position 127, cf. [5], Figure 1. The backbone of the RNA molecule is drawn as straight lineswhile base pairings are shown...

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Recommended Reading

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Authors and Affiliations

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

    Rune B. Lyngsø

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  1. Rune B. Lyngsø
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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 Including Pseudoknots. In: Kao, MY. (eds) Encyclopedia of Algorithms. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-30162-4_346

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