Publication:1025221

DOI10.1016/J.MBS.2008.12.011zbMATH Open1194.92025arXiv0807.0689OpenAlexW2102428566WikidataQ51835541 ScholiaQ51835541MaRDI QIDQ1025221FDOQ1025221

Hillary S. W. Han, Christian M. Reidys

Publication date: 18 June 2009

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

Abstract: In this paper we study the distribution of stacks in $k$-noncrossing, $au$-canonical RNA pseudoknot structures ($<k,au>$-structures). An RNA structure is called $k$-noncrossing if it has no more than $k-1$ mutually crossing arcs and $au$-canonical if each arc is contained in a stack of length at least $au$. Based on the ordinary generating function of $<k,au>$-structures cite{Reidys:08ma} we derive the bivariate generating function $$, where ${sfT}_{k,au}(n,t)$ is the number of $<k,au>$-structures having exactly $t$ stacks and study its singularities. We show that for a certain parametrization of the variable $u$, $$ has a unique, dominant singularity. The particular shift of this singularity parametrized by $u$ implies a central limit theorem for the distribution of stack-numbers. Our results are of importance for understanding the ``language of minimum-free energy RNA pseudoknot structures, generated by computer folding algorithms.

Full work available at URL: https://arxiv.org/abs/0807.0689

zbMATH Keywords

central limit theoremgenerating functionstacksingularity analysispseudoknot\(k\)-non-crossing RNA structure

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Central limit and other weak theorems (60F05) Computer aspects of numerical algorithms (65Y99)

Cites Work

• Title not available (Why is that?)
• Title not available (Why is that?)
• Differentiably finite power series
• Central and local limit theorems applied to asymptotic enumeration
• Tree adjoining grammars for RNA structure prediction
• Crossings and nestings of matchings and partitions
• Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
• Singularity analysis, Hadamard products, and tree recurrences
• Combinatorics of RNA structures with pseudoknots
• An Efficient Implementation of Edmonds' Algorithm for Maximum Matching on Graphs
• Random walks in Weyl chambers and the decomposition of tensor powers
• Boltzmann Samplers for the Random Generation of Combinatorial Structures
• Linear trees and RNA secondary structure
• Computation of Generating Functions for Biological Molecules
• Combinatorics of RNA Hairpins and Cloverleaves
• Predicting RNA secondary structures with pseudoknots by MCMC sampling
• Combinatorial design of pseudoknot RNA

Cited In (1)

• A folding ``framework structure of \textit{Tetrahymena} group I intron

This page was built for publication: Stacks in canonical RNA pseudoknot structures

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q1025221)