title: Shapes of interacting RNA complexes.
abstract: Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops. This shape projection preserves the topological core of the RNA complex, and for fixed topological genus there are only finitely many such shapes. Our main result is a new bijection that relates the shapes of RNA complexes with shapes of RNA structures. This allows for computing the shape polynomial of RNA complexes via the shape polynomial of RNA structures. We furthermore present a linear time uniform sampling algorithm for shapes of RNA complexes of fixed topological genus.
authors: Department of Mathematics and Computer Science, University of Southern Denmark , Odense M, Denmark .
authors: Benjamin M M
authors: BM
authors: Fu
authors: Christian M
authors: CM
authors: Reidys
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D006860:Hydrogen Bonding; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA
keywords: bijection; interacting RNA complexes; shape polynomials; topological genus; uniform generation