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Prediction of RNA secondary structures with pseudoknots

Author

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  • Bon, M.
  • Orland, H.

Abstract

We present a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. The algorithm utilizes a simplified parametrization of the free energies for pair stacking, loop penalties, etc. and in addition a free energy penalty proportional to the topological genus of the pairing graph. Our method can take into account all pseudoknot topologies and achieves high success rates compared to state-of-the-art methods. This shows that the genus is a promising concept to classify pseudoknots.

Suggested Citation

  • Bon, M. & Orland, H., 2010. "Prediction of RNA secondary structures with pseudoknots," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(15), pages 2987-2992.
    • Handle: RePEc:eee:phsmap:v:389:y:2010:i:15:p:2987-2992
    DOI: 10.1016/j.physa.2010.02.046
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    Cited by:

    1. Nicolò Cangiotti, 2024. "Feynman Diagrams beyond Physics: From Biology to Economy," Mathematics, MDPI, vol. 12(9), pages 1-17, April.

    More about this item

    Keywords

    Biopolymers; Knots;

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