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 . Furthermore we outline how shapes can be used in order to extract essential information of RNA structure databases.
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Cites work
- scientific article; zbMATH DE number 3900794 (Why is no real title available?)
- scientific article; zbMATH DE number 919921 (Why is no real title available?)
- scientific article; zbMATH DE number 3246034 (Why is no real title available?)
- A new combinatorial identity for unicellular maps, via a direct bijective approach
- Boltzmann Samplers for the Random Generation of Combinatorial Structures
- Exact-size sampling for Motzkin trees in linear time via Boltzmann samplers and holonomic specification
- Fatgraph models of proteins
- Generation of RNA pseudoknot structures with topological genus filtration
- RNA folding and large \(N\) matrix theory
- Spaces of RNA secondary structures
- The Euler characteristic of the moduli space of curves
- The chromatic polynomial of fatgraphs and its categorification
- Topological classification and enumeration of RNA structures by genus
Cited in
(14)- A generalisation of the Kauffman bracket polynomial to determine and analyse structural elements in a RNA secondary structure
- Generation of RNA pseudoknot structures with topological genus filtration
- Topological classification and enumeration of RNA structures by genus
- A new algorithm for generation of different types of RNA
- On RNA-RNA interaction structures of fixed topological genus
- Loop homology of bi-secondary structures
- Posets and spaces of \(k\)-noncrossing RNA structures
- Moduli spaces and macromolecules
- Statistics of topological RNA structures
- Topological language for RNA
- 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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