Shapes of topological RNA structures

DOI10.1016/J.MBS.2015.10.004zbMATH Open1364.92029arXiv1403.2908OpenAlexW2963708209WikidataQ45020806 ScholiaQ45020806MaRDI QIDQ899333FDOQ899333

Christian M. Reidys, Fenix W. D. Huang

Publication date: 28 December 2015

Published in: Mathematical Biosciences (Search for Journal in Brave)

Abstract: A topological RNA structure is derived from a diagram and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological, information and for fixed topological genus there exist only finitely many such shapes. We shall express topological RNA structures as unicellular maps, i.e. graphs together with a cyclic ordering of their half-edges. In this paper we prove a bijection of shapes of topological RNA structures. We furthermore derive a linear time algorithm generating shapes of fixed topological genus. We derive explicit expressions for the coefficients of the generating polynomial of these shapes and the generating function of RNA structures of genus $g$. Furthermore we outline how shapes can be used in order to extract essential information of RNA structure databases.

Full work available at URL: https://arxiv.org/abs/1403.2908

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zbMATH Keywords

treegenerating functiongenusuniform generationRNA shape

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Computational methods for problems pertaining to biology (92-08)

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Cited In (9)

• Posets and Spaces of $k$-Noncrossing RNA Structures
• On RNA-RNA interaction structures of fixed topological genus
• Loop homology of bi-secondary structures
• Moduli spaces and macromolecules
• Statistics of topological RNA structures
• HYPERMATRIX ALGEBRA AND IRREDUCIBLE ARITY IN HIGHER-ORDER SYSTEMS: CONCEPTS AND PERSPECTIVES
• Topological Classification of RNA Structures via Intersection Graph
• Loop homology of bi-secondary structures. II
• The block spectrum of RNA pseudoknot structures

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