Superbubbles as an Empirical Characteristic of Directed Networks

Abstract: Superbubbles are acyclic induced subgraphs of a digraph with single entrance and exit that naturally arise in the context of genome assembly and the analysis of genome alignments in computational biology. These structures can be computed in linear time and are confined to non-symmetric digraphs. We demonstrate empirically that graph parameters derived from superbubbles provide a convenient means of distinguishing different classes of real-world graphical models, while being largely unrelated to simple, commonly used parameters.