2014/05/14 by Benjamin Mingming Fu, Benjamin MingMing Fu, Fu, Benjamin MingMing +2
Biochemistry, Genetics and Molecular Biology · Mathematics · #05A19 and 92E10 #Biomolecules (q-bio.BM) #Combinatorics (math.CO) #FOS: Biological sciences #FOS: Mathematics #Genomics and Chromatin Dynamics #RNA Research and Splicing #RNA and protein synthesis mechanisms #math.CO #msc:05A19 #msc:92E10 #q-bio.BM
paper · pdf · doi:10.48550/arxiv.1405.3390
38 pages 24 figures
openalex publication_date 2014/05/14 · arxiv created 2014/05/20 · arxiv updated 2014/05/22 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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 to compute 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.