Uniform generation of RNA-RNA interaction structures of fixed topological genus

TL;DR

This paper introduces a bijection and a linear-time uniform sampling algorithm for RNA-RNA interaction structures of fixed topological genus, advancing the understanding and modeling of complex RNA interactions.

Contribution

It provides a novel bijection and an efficient algorithm for generating RNA complexes of fixed genus, along with a decomposition grammar and statistical analysis.

Findings

Linear-time uniform sampling of RNA complexes of fixed genus

Explicit bijection for RNA-RNA interaction structures

Comparison of topological RNA complexes with biological data

Abstract

Interacting RNA complexes are studied via bicellular maps using a filtration via their topological genus. Our main result is a new bijection for RNA-RNA interaction structures and linear time uniform sampling algorithm for RNA complexes of fixed topological genus. The bijection allows to either reduce the topological genus of a bicellular map directly, or to lose connectivity by decomposing the complex into a pair of single stranded RNA structures. Our main result is proved bijectively. It provides an explicit algorithm of how to rewire the corresponding complexes and an unambiguous decomposition grammar. Using the concept of genus induction, we construct bicellular maps of fixed topological genus $g$ uniformly in linear time. We present various statistics on these topological RNA complexes and compare our findings with biological complexes. Furthermore we show how to construct loop-energy based complexes using our decomposition grammar.