Extending the Overlap Graph for Gene Assembly in Ciliates

TL;DR

This paper extends the overlap graph concept to create a graph rewriting system for simple gene assembly in ciliates, simplifying the process and providing characterizations of rule power, bridging string and graph models.

Contribution

It introduces a graph rewriting system for simple gene assembly, simplifying existing string models and establishing equivalence between the two approaches.

Findings

Graph rewriting system is less involved than string rewriting.

Characterizations of the power of graph rewriting rules.

Equivalence established between string and graph rewriting systems.

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.