title: Asymptotics of RNA shapes.
abstract: RNA shapes, introduced by Giegerich et al. (2004), 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 (Steffen et al., 2006; Voss et al., 2006), 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.
authors.affiliation: Biology Department, Boston College, Chestnut Hill, MA 02467, USA. lorenzwi@bc.edu
authors.forename: W A
authors.initials: WA
authors.lastname: Lorenz
authors.forename: Y
authors.initials: Y
authors.lastname: Ponty
authors.forename: P
authors.initials: P
authors.lastname: Clote
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA