REDUCTION GRAPHS FROM OVERLAP GRAPHS FOR GENE ASSEMBLY IN CILIATES

Abstract

Ciliates are unicellular organisms having two types of functionally different nuclei: micronucleus and macronucleus. Gene assembly transforms a micronucleus into a macronucleus, thereby transforming each gene from its micronuclear form to its macronuclear form. Within a formal intramolecular model of gene assembly based on strings, the notion of reduction graph represents the macronuclear form of a gene, including byproducts, given only a description of the micronuclear form of that gene. For a more abstract model of gene assembly based on graphs, one cannot, in general, define the notion of reduction graphs. We show that if we restrict ourselves to the so-called realistic overlap graphs (which correspond to genes occurring in nature), then the notion of reduction graph can be defined in a manner equivalent to the string model. This allows one to carry over from the string model to the graph model several results that rely on the notion of reduction graph.