Small-world networks and RNA secondary structures

Defne Surujon 1 Yann Ponty 2, 3, 4 Peter Clote 1, *
* Corresponding author
4 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : Let $S_n$ denote the network of all RNA secondary structures of length $n$, in which undirected edges exist between structures $s$, $t$ such that $t$ is obtained from $s$ by the addition, removal or shift of a single base pair. Using context-free grammars, generating functions and complex analysis, we show that the asymptotic average degree is $O(n)$ and that the asymptotic clustering coefficient is $O(1/n)$, from which it follows that the family $S_n$, $n = 1, 2, 3,\ldots$ of secondary structure networks is not small-world.
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Defne Surujon, Yann Ponty, Peter Clote. Small-world networks and RNA secondary structures. Journal of computational biology : a journal of computational molecular cell biology, Mary Ann Liebert 2019, 26 (1), pp.16--26. ⟨10.1089/cmb.2018.0125⟩. ⟨hal-01424452v2⟩



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