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
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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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DOI: https://doi.org/10.1007/978-0-387-30162-4_346
Publisher Name: Springer, Boston, MA
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