Expected distance between terminal nucleotides of RNA secondary structures

DOI10.1007/S00285-011-0467-8MaRDI QIDQ455765zbMATH OpenOpenAlexWikidataFDO

Authors Peter Clote, Yann Ponty, Jean-Marc Steyaert

Publication date 22 October 2012

Published in Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://hal.inria.fr/inria-00619921/file/paper.pdf

zbMATH Keywords

dynamic programmingRNAasymptotic combinatoricsBoltzmann partition function

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Dynamic programming (90C39) Enumeration in graph theory (05C30) Dynamic programming in optimal control and differential games (49L20)

Recommendations

• Asymptotic expected number of base pairs in optimal secondary structure for random RNA using the Nussinov--Jacobson energy model
• Asymptotic number of hairpins of saturated RNA secondary structures
• General combinatorics of RNA secondary structure
• Investigation of the Bernoulli model for RNA secondary structures
• The end-to-end distance of RNA as a randomly self-paired polymer

Cites work

• scientific article; zbMATH DE number 3311755 (Why is no real title available?)
• Analytic combinatorics
• Combinatorics of RNA secondary structures
• On some new sequences generalizing the Catalan and Motzkin numbers

Cited in

(7)

• RNA secondary structures with given motif specification: combinatorics and algorithms
• Formulae and asymptotics for coefficients of algebraic functions
• ViennaRNA
• The block spectrum of RNA pseudoknot structures
• The end-to-end distance of RNA as a randomly self-paired polymer
• The rainbow spectrum of RNA secondary structures
• Asymptotic distribution of motifs in a stochastic context-free grammar model of RNA folding

Describes a project that uses

Uses Software

• Rfam
• RNAfold
• RNAsubopt
• Mfold
• VARNA

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