Generation of RNA pseudoknot structures with topological genus filtration

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

Fenix W. D. Huang, Christian M. Reidys, Markus E. Nebel

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

Recommendations

• Shapes of topological RNA structures
• Topological language for RNA
• The topological filtration of \(\gamma\)-structures
• Statistics of topological RNA structures
• RNA secondary structures: an approach through pseudoknots and fatgraphs

zbMATH Keywords

samplingpartition functionRNA pseudoknot structuretopological surfaceRNA secondary structuretopological genus

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

Cites Work

• Title not available (Why is that?)
• Topological classification and enumeration of RNA structures by genus
• Title not available (Why is that?)
• Crossings and nestings of matchings and partitions
• RNA folding and large \(N\) matrix theory
• Random k -noncrossing RNA structures
• Spaces of RNA secondary structures
• The chromatic polynomial of fatgraphs and its categorification
• Fatgraph models of proteins
• Title not available (Why is that?)
• 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
• A calculus for the random generation of labelled combinatorial structures
• Combinatorics of RNA Hairpins and Cloverleaves
• Title not available (Why is that?)

Cited In (8)

• 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

This page was built for publication: Generation of RNA pseudoknot structures with topological genus filtration

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2437014)