Asymptotics of RNA shapes - Inria - Institut national de recherche en sciences et technologies du numérique Access content directly
Journal Articles Journal of Computational Biology Year : 2008

Asymptotics of RNA shapes


RNA shapes, introduced by Giegerich et al., provide a useful classification of the branching complexity for RNA secondary structures. In this paper, we derive an exact value for the asymptotic number of RNA shapes, by relying on an elegant relation between non-ambiguous, context-free grammars and generating functions. Our results provide a theoretical upper bound on the length of RNA sequences amenable to probabilistic shape analysis, under the assumption that any base can basepair with any other base. Since the relation between context-free grammars and asymptotic enumeration is simple yet not well-known in bioinformatics, we give a self-contained presentation with illustrative examples. Additionally, we prove a surprising 1-to-1 correspondence between Pi-shapes and Motzkin numbers
Not file

Dates and versions

inria-00548861 , version 1 (20-12-2010)



William Andrew Lorenz, Peter Clote, Yann Ponty. Asymptotics of RNA shapes. Journal of Computational Biology, 2008, 15 (1), pp.31--63. ⟨10.1089/cmb.2006.0153⟩. ⟨inria-00548861⟩
115 View
0 Download



Gmail Facebook Twitter LinkedIn More