Improved RNA pseudoknots prediction and classification using a new topological invariant

Abstract : We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both I) the topological genus of the graph and II) the number of crossing arcs of the corresponding primitive graph. We add a term proportional to these topological invariants to the standard free energy of the RNA molecule, thus obtaining a novel free energy parametrization which takes into account the abundance of topologies of RNA pseudoknots observed in RNA databases.
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Submitted on : Tuesday, June 7, 2016 - 11:04:02 AM
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  • HAL Id : cea-01327864, version 1
  • ARXIV : 1605.04825

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Graziano Vernizzi, Henri Orland, A. Zee. Improved RNA pseudoknots prediction and classification using a new topological invariant. 2016. ⟨cea-01327864⟩

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