title: Combinatorics of RNA structures with pseudoknots.
abstract: In this paper, we derive the generating function of RNA structures with pseudoknots. We enumerate all k-noncrossing RNA pseudoknot structures categorized by their maximal sets of mutually intersecting arcs. In addition, we enumerate pseudoknot structures over circular RNA. For 3-noncrossing RNA structures and RNA secondary structures we present a novel 4-term recursion formula and a 2-term recursion, respectively. Furthermore, we enumerate for arbitrary k all k-noncrossing, restricted RNA structures i.e. k-noncrossing RNA structures without 2-arcs i.e. arcs of the form (i,i+2), for 1< or =i< or =n-2.
authors: Center for Combinatorics, LMPC-TJKLC, Nankai University, Tianjin 300071, China.
authors: Emma Y
authors: EY
authors: Jin
authors: Jing
authors: J
authors: Qin
authors: Christian M
authors: CM
authors: Reidys
mesh_terms: D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA