Generation of RNA pseudoknot structures with topological genus filtration

DOI10.1016/J.MBS.2013.07.014zbMATH Open1308.92078arXiv1304.7397OpenAlexW2076175048WikidataQ45769514 ScholiaQ45769514MaRDI QIDQ2437014FDOQ2437014

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)

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.

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

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zbMATH Keywords

samplingpartition functionRNA pseudoknot structuretopological surfaceRNA secondary structuretopological genus

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

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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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