Topological classification and enumeration of RNA structures by genus (Q378306): Difference between revisions
From MaRDI portal
Created a new Item |
ReferenceBot (talk | contribs) Changed an Item |
||
(7 intermediate revisions by 6 users not shown) | |||
Property / author | |||
Property / author: Robert C. Penner / rank | |||
Property / author | |||
Property / author: Michael S. Waterman / rank | |||
Property / author | |||
Property / author: Robert C. Penner / rank | |||
Normal rank | |||
Property / author | |||
Property / author: Michael S. Waterman / rank | |||
Normal rank | |||
Property / review text | |||
The authors study the association between RNA pseudoknot structures and topological surfaces, and the classification of the former by the genus of the latter. On the basis of earlier work [\textit{J. Harer} and \textit{D. Zagier}, Invent. Math. 85, 457--485 (1986; Zbl 0616.14017)], they calculate the generating function for the number of structures with a fixed genus and number of nucleotides, and given minimum stack size so that no two consecutive nucleotides are base-paired. In particular, they show that the generating function is algebraic, and they prove that for stack size at least two, the genus of the surface only enters sub-exponentially; hence, they argue that, for any genus, the resulting slow growth rates with respect to RNA molecule numbers imply the existence of neutral networks [\textit{C. Reidys} et al., Bull. Math. Biol. 59, No. 2, 339--397 (1997; Zbl 0925.92006)]. Specific structures known as shapes are shown to be in a one-to-one correspondence with cells in the Penner-Strebel decomposition [\textit{R.C. Penner}, Commun. Math. Phys. 113, 299--339 (1987; Zbl 0642.32012)] of Riemann's moduli space of a surface with a given genus and one boundary component. | |||
Property / review text: The authors study the association between RNA pseudoknot structures and topological surfaces, and the classification of the former by the genus of the latter. On the basis of earlier work [\textit{J. Harer} and \textit{D. Zagier}, Invent. Math. 85, 457--485 (1986; Zbl 0616.14017)], they calculate the generating function for the number of structures with a fixed genus and number of nucleotides, and given minimum stack size so that no two consecutive nucleotides are base-paired. In particular, they show that the generating function is algebraic, and they prove that for stack size at least two, the genus of the surface only enters sub-exponentially; hence, they argue that, for any genus, the resulting slow growth rates with respect to RNA molecule numbers imply the existence of neutral networks [\textit{C. Reidys} et al., Bull. Math. Biol. 59, No. 2, 339--397 (1997; Zbl 0925.92006)]. Specific structures known as shapes are shown to be in a one-to-one correspondence with cells in the Penner-Strebel decomposition [\textit{R.C. Penner}, Commun. Math. Phys. 113, 299--339 (1987; Zbl 0642.32012)] of Riemann's moduli space of a surface with a given genus and one boundary component. / rank | |||
Normal rank | |||
Property / Mathematics Subject Classification ID | |||
Property / Mathematics Subject Classification ID: 92D20 / rank | |||
Normal rank | |||
Property / zbMATH DE Number | |||
Property / zbMATH DE Number: 6225311 / rank | |||
Normal rank | |||
Property / zbMATH Keywords | |||
RNA structure | |||
Property / zbMATH Keywords: RNA structure / rank | |||
Normal rank | |||
Property / zbMATH Keywords | |||
topological surface | |||
Property / zbMATH Keywords: topological surface / rank | |||
Normal rank | |||
Property / zbMATH Keywords | |||
genus | |||
Property / zbMATH Keywords: genus / rank | |||
Normal rank | |||
Property / zbMATH Keywords | |||
generating function | |||
Property / zbMATH Keywords: generating function / rank | |||
Normal rank | |||
Property / zbMATH Keywords | |||
neutral network | |||
Property / zbMATH Keywords: neutral network / rank | |||
Normal rank | |||
Property / zbMATH Keywords | |||
Penner-Strebel decomposition | |||
Property / zbMATH Keywords: Penner-Strebel decomposition / rank | |||
Normal rank | |||
Property / Wikidata QID | |||
Property / Wikidata QID: Q44396933 / rank | |||
Normal rank | |||
Property / reviewed by | |||
Property / reviewed by: Nikola Popović / rank | |||
Normal rank | |||
Property / MaRDI profile type | |||
Property / MaRDI profile type: MaRDI publication profile / rank | |||
Normal rank | |||
Property / full work available at URL | |||
Property / full work available at URL: https://doi.org/10.1007/s00285-012-0594-x / rank | |||
Normal rank | |||
Property / OpenAlex ID | |||
Property / OpenAlex ID: W2029235587 / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Finite type invariants and fatgraphs / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: The Poisson structure on the moduli space of flat connections and chord diagrams / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Quantization of the algebra of chord diagrams / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: On the Vassiliev knot invariants / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Lie algebras and the four color theorem / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: The asymptotic number of tree-rooted maps on a surface / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Invariant tensor formulas via chord diagrams / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Combinatorial aspects of continued fractions / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Sequence of operations analysis for dynamic data structures / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Q3549563 / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: A direct bijection for the Harer-Zagier formula / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Factoring \(n\)-cycles and counting maps of given genus / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: The Euler characteristic of the moduli space of curves / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: RNA structures with pseudo-knots: graph-theoretical, combinatorial, and statistical properties / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Random induced subgraphs of Cayley graphs induced by transpositions / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Q4273352 / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Q4273591 / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: RNA folding and large \(N\) matrix theory / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: The decorated Teichmüller space of punctured surfaces / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Perturbative series and the moduli space of Riemann surfaces / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Weil-Petersson volumes / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Combinatorics of RNA Hairpins and Cloverleaves / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Fatgraph models of proteins / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Spaces of RNA secondary structures / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Combinatorial Computational Biology of RNA / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Modular, \(k\)-noncrossing diagrams / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Generic properties of combinatory maps: Neutral networks of RNA secondary structures / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Combinatorial Landscapes / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Replication and mutation on neutral networks / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Large components in random induced subgraphs of \(n\)-cubes / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Q4344108 / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Q3338499 / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Q3872468 / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Computation of Generating Functions for Biological Molecules / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Linear trees and RNA secondary structure / rank | |||
Normal rank | |||
Property / cites work | |||
Property / cites work: Q4315008 / rank | |||
Normal rank | |||
links / mardi / name | links / mardi / name | ||
Latest revision as of 01:41, 7 July 2024
scientific article
Language | Label | Description | Also known as |
---|---|---|---|
English | Topological classification and enumeration of RNA structures by genus |
scientific article |
Statements
Topological classification and enumeration of RNA structures by genus (English)
0 references
11 November 2013
0 references
The authors study the association between RNA pseudoknot structures and topological surfaces, and the classification of the former by the genus of the latter. On the basis of earlier work [\textit{J. Harer} and \textit{D. Zagier}, Invent. Math. 85, 457--485 (1986; Zbl 0616.14017)], they calculate the generating function for the number of structures with a fixed genus and number of nucleotides, and given minimum stack size so that no two consecutive nucleotides are base-paired. In particular, they show that the generating function is algebraic, and they prove that for stack size at least two, the genus of the surface only enters sub-exponentially; hence, they argue that, for any genus, the resulting slow growth rates with respect to RNA molecule numbers imply the existence of neutral networks [\textit{C. Reidys} et al., Bull. Math. Biol. 59, No. 2, 339--397 (1997; Zbl 0925.92006)]. Specific structures known as shapes are shown to be in a one-to-one correspondence with cells in the Penner-Strebel decomposition [\textit{R.C. Penner}, Commun. Math. Phys. 113, 299--339 (1987; Zbl 0642.32012)] of Riemann's moduli space of a surface with a given genus and one boundary component.
0 references
RNA structure
0 references
topological surface
0 references
genus
0 references
generating function
0 references
neutral network
0 references
Penner-Strebel decomposition
0 references
0 references