Extending the Overlap Graph for Gene Assembly in Ciliates

Abstract

Abstract. Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been introduced. This restriction has subsequently been defined as a string rewriting system. We show that by extending the notion of overlap graph it is possible to define a graph rewriting system for two of the three types of rules that make up simple gene assembly. It turns out that this graph rewriting system is less involved than its corresponding string rewriting system. Finally, we give characterizations of the 'power' of both types of graph rewriting rules. Because of the equivalence of these string and graph rewriting systems, the given characterizations can be carried over to the string rewriting system.

Computational Nature of Gene Assembly in Ciliates

“…We only give here the definitions for the stringbased operations, where the mathematical formulation is more concise. For the other formulations, including the relationships among these models, we refer to [46,63,8].…”

Combining overlap and containment for gene assembly in ciliates

“…While this characterization is based on extended overlap graphs, due to its equivalence, it can be carried over to the string rewriting system for simple gene assembly. An extended abstract containing selected results of this paper was presented at LATA'08 [9].…”