The topological filtration of -structures

DOI10.1016/J.MBS.2012.09.006MaRDI QIDQ1935133zbMATH OpenOpenAlexWikidataFDO

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

Publication date 30 January 2013

Published in Mathematical Biosciences (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1202.1061, https://portal.findresearcher.sdu.dk/da/publications/cb98e087-d9e5-4e1a-84ab-0b7a84f0e404

zbMATH Keywords

\(\gamma\)-structurecentral limit theoremgenerating functiongenus filtrationirreducible shadowsingularity analysis

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

Abstract: In this paper we study $gamma$-structures filtered by topological genus. $gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A $gamma$-structure is composed by specific building blocks, that have topological genus less than or equal to $gamma$, where composition means concatenation and nesting of such blocks. Our main results are the derivation of a new bivariate generating function for $gamma$-structures via symbolic methods, the singularity analysis of the solutions and a central limit theorem for the distribution of topological genus in $gamma$-structures of given length. In our derivation specific bivariate polynomials play a central role. Their coefficients count particular motifs of fixed topological genus and they are of relevance in the context of genus recursion and novel folding algorithms.

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Cited in

(8)

• The block spectrum of RNA pseudoknot structures
• Statistics of topological RNA structures
• Generation of RNA pseudoknot structures with topological genus filtration
• Moduli spaces and macromolecules
• scientific article; zbMATH DE number 3857278 (Why is no real title available?)
• scientific article; zbMATH DE number 58367 (Why is no real title available?)
• Augmented Γ-spaces, the stable rank filtration, and a bu analogue of the Whitehead conjecture
• Shapes of topological RNA structures

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