Combinatorics of RNA structures with pseudoknots

DOI10.1007/s11538-007-9240-yzbMath1281.92055arXiv0704.2518OpenAlexW2091599083WikidataQ51905216 ScholiaQ51905216MaRDI QIDQ2426390

Christian M. Reidys, Jing Qin, Emma Yu Jin

Publication date: 22 April 2008

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

Full work available at URL: https://arxiv.org/abs/0704.2518

zbMATH Keywords

generating functionenumerationreflection principlewalksRNA secondary structurepseudoknotWeyl-chamber

Mathematics Subject Classification ID

Related Items (26)

Regular simple queues of protein contact maps ⋮ Algebraic dynamic programming for multiple context-free grammars ⋮ Local connectivity of neutral networks ⋮ Irreducibility in RNA structures ⋮ A generating tree approach to \(k\)-nonnesting partitions and permutations ⋮ A simple bijection for enhanced, classical, and 2-distant \(k\)-noncrossing partitions ⋮ Posets and Spaces of $k$-Noncrossing RNA Structures ⋮ The vectorial kernel method for walks with longer steps ⋮ Transformations of partial matchings ⋮ Enumeration of symmetric arc diagrams ⋮ Generating functions for lattice paths with several forbidden patterns ⋮ Symmetric circular matchings and RNA folding ⋮ Asymptotic enumeration of RNA structures with pseudoknots ⋮ Fatgraph models of RNA structure ⋮ RNA pseudoknot structures with arc-length \(\geq 3\) and stack-length \(\geq \sigma \) ⋮ Controlled non-uniform random generation of decomposable structures ⋮ Loop homology of bi-secondary structures ⋮ Neutral networks of sequence to shape maps ⋮ Central and local limit theorems for RNA structures ⋮ Statistics of canonical RNA pseudoknot structures ⋮ Random k -noncrossing RNA structures ⋮ Combinatorial design of pseudoknot RNA ⋮ Analytic combinatorics of lattice paths with forbidden patterns, the vectorial kernel method, and generating functions for pushdown automata ⋮ Stacks in canonical RNA pseudoknot structures ⋮ On the decomposition of \(k\)-noncrossing RNA structures ⋮ Loop homology of bi-secondary structures. II

Cites Work

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• Tree adjoining grammars for RNA structure prediction
• Combinatorics of RNA secondary structures
• Spaces of RNA secondary structures
• Linear trees and RNA secondary structure
• Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
• Crossings and nestings of matchings and partitions
• Computation of Generating Functions for Biological Molecules
• Random Walk in a Weyl Chamber
• Combinatorics of RNA Hairpins and Cloverleaves
• On the Vector Representations of Induced Matroids

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