Topological classification and enumeration of RNA structures by genus (Q378306): Difference between revisions
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Property / author: Jørgen Ellegaard Andersen / rank | |||
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Property / author: Christian M. Reidys / rank | |||
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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 | |||
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Property / reviewed by: Nikola Popović / rank | |||
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Property / Mathematics Subject Classification ID: 92D20 / rank | |||
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Property / zbMATH DE Number | |||
Property / zbMATH DE Number: 6225311 / rank | |||
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Property / zbMATH Keywords | |||
RNA structure | |||
Property / zbMATH Keywords: RNA structure / rank | |||
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topological surface | |||
Property / zbMATH Keywords: topological surface / rank | |||
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genus | |||
Property / zbMATH Keywords: genus / rank | |||
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generating function | |||
Property / zbMATH Keywords: generating function / rank | |||
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neutral network | |||
Property / zbMATH Keywords: neutral network / rank | |||
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Penner-Strebel decomposition | |||
Property / zbMATH Keywords: Penner-Strebel decomposition / rank | |||
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Revision as of 12:06, 29 June 2023
scientific article
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English | Topological classification and enumeration of RNA structures by genus |
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Statements
Topological classification and enumeration of RNA structures by genus (English)
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11 November 2013
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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.
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RNA structure
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topological surface
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genus
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generating function
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neutral network
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Penner-Strebel decomposition
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