On RNA-RNA interaction structures of fixed topological genus

DOI10.1016/J.MBS.2014.12.008zbMATH Open1311.05020arXiv1311.0684OpenAlexW1963786121WikidataQ46779199 ScholiaQ46779199MaRDI QIDQ2344602FDOQ2344602

Authors: Benjamin M. M. Fu, Hillary S. W. Han, Christian M. Reidys 

Publication date: 15 May 2015

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

Abstract: Interacting RNA complexes are studied via bicellular maps using a filtration via their topological genus. Our main result is a new bijection for RNA-RNA interaction structures and linear time uniform sampling algorithm for RNA complexes of fixed topological genus. The bijection allows to either reduce the topological genus of a bicellular map directly, or to lose connectivity by decomposing the complex into a pair of single stranded RNA structures. Our main result is proved bijectively. It provides an explicit algorithm of how to rewire the corresponding complexes and an unambiguous decomposition grammar. Using the concept of genus induction, we construct bicellular maps of fixed topological genus $g$ uniformly in linear time. We present various statistics on these topological RNA complexes and compare our findings with biological complexes. Furthermore we show how to construct loop-energy based complexes using our decomposition grammar.

Full work available at URL: https://arxiv.org/abs/1311.0684

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zbMATH Keywords

decompositionnon-uniform samplingtopological genusuniform generationbicellular mapRNA-RNA interaction structure

Mathematics Subject Classification ID

Combinatorial identities, bijective combinatorics (05A19) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

Cites Work

• The structure of unicellular maps, and a connection between maps of positive genus and planar labelled trees
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• RNA folding and large \(N\) matrix theory
• Spaces of RNA secondary structures
• Generation of RNA pseudoknot structures with topological genus filtration
• Fatgraph models of proteins
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• Algorithms for Loop Matchings
• Boltzmann Samplers for the Random Generation of Combinatorial Structures
• Proportions of Irreducible Diagrams
• A new combinatorial identity for unicellular maps, via a direct bijective approach
• Combinatorics of RNA Hairpins and Cloverleaves
• Modular, \(k\)-noncrossing diagrams
• Large-\(N\) random matrices for RNA folding
• RNA secondary structures and their prediction
• Shapes of topological RNA structures

Uses Software

• starBase

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