Combinatorial analysis of interacting RNA molecules

DOI10.1016/J.MBS.2011.04.009zbMATH Open1226.92021arXiv1006.4089OpenAlexW1964884881WikidataQ51556109 ScholiaQ51556109MaRDI QIDQ648014FDOQ648014

Authors: Thomas J. X. Li, Christian M. Reidys 

Publication date: 22 November 2011

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

Abstract: Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with two backbones drawn horizontally on top of each other such that (1) intramolecular and intermolecular bonds are noncrossing and (2) there is no "zig-zag" configuration. This paper studies joint structures with arc-length at least four in which both, interior and exterior stack-lengths are at least two (no isolated arcs). The key idea in this paper is to consider a new type of shape, based on which joint structures can be derived via symbolic enumeration. Our results imply simple asymptotic formulas for the number of joint structures with surprisingly small exponential growth rates. They are of interest in the context of designing prediction algorithms for RNA-RNA interactions.

Full work available at URL: https://arxiv.org/abs/1006.4089

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zbMATH Keywords

shapesingularity analysisRNA interactionRNA secondary structurejoint structuresymbolic enumeration

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Symbolic computation and algebraic computation (68W30) Computational methods for problems pertaining to biology (92-08)

Cites Work

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• Research in Computational Molecular Biology
• RNA secondary structure: a complete mathematical analysis
• Linear trees and RNA secondary structure
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• Combinatorics of RNA-RNA interaction
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Cited In (15)

• Parametric analysis of RNA branching configurations
• Making multiple RNA interaction practical
• Gibbs/MCMC sampling for multiple RNA interaction with sub-optimal solutions
• Research in Computational Molecular Biology
• A grammatical approach to RNA-RNA interaction prediction
• NEUTRAL NETWORKS OF INTERACTING RNA SECONDARY STRUCTURES
• Statistics of topological RNA structures
• Combinatorics of RNA-RNA interaction
• Asymptotic number of hairpins of saturated RNA secondary structures
• Thermodynamic Analysis of Interacting Nucleic Acid Strands
• Automated prediction of three-way junction topological families in RNA secondary structures
• Using temperature effects to predict the interactions between two RNAs
• Symmetric circular matchings and RNA folding
• The block spectrum of RNA pseudoknot structures
• Fatgraph models of RNA structure

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