Prediction of RNA secondary structures with pseudoknots

M. Bon and H. Orland

Physica A: Statistical Mechanics and its Applications, 2010, vol. 389, issue 15, 2987-2992

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.

Keywords: Biopolymers; Knots (search for similar items in EconPapers)
Date: 2010
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Citations: View citations in EconPapers (1)

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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:389:y:2010:i:15:p:2987-2992

DOI: 10.1016/j.physa.2010.02.046

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