Generation of RNA pseudoknot structures with topological genus filtration

DOI10.1016/J.MBS.2013.07.014MaRDI QIDQ2437014zbMATH OpenOpenAlexWikidataFDO

Authors Fenix W. D. Huang, Markus E. Nebel, Christian M. Reidys

Publication date 27 February 2014

Published in Mathematical Biosciences (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1304.7397

zbMATH Keywords

samplingpartition functionRNA pseudoknot structuretopological surfaceRNA secondary structuretopological genus

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

Abstract: In this paper we present a sampling framework for RNA structures of fixed topological genus. We introduce a novel, linear time, uniform sampling algorithm for RNA structures of fixed topological genus $g$, for arbitrary $g>0$. Furthermore we develop a linear time sampling algorithm for RNA structures of fixed topological genus $g$ that are weighted by a simplified, loop-based energy functional. For this process the partition function of the energy functional has to be computed once, which has $O(n^2)$ time complexity.

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Cites work

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Cited in

(10)

• Topological classification and enumeration of RNA structures by genus
• On RNA-RNA interaction structures of fixed topological genus
• Moduli spaces and macromolecules
• Statistics of topological RNA structures
• Shapes of topological RNA structures
• Topological language for RNA
• Pseudoknot-generating operation
• Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy
• Topological Classification of RNA Structures via Intersection Graph
• Random k-noncrossing RNA structures

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