Breakpoint graphs for gene assembly in ciliates
Gene assembly is a very involved DNA transformation process which occurs in an extremely old group of organisms called stichotrichous ciliates. The process transforms one nucleus, the micronucleus, into a radically different nucleus, the macronucleus. Sound formal models have been developed for this process based on string rewriting and graph rewriting. Another popular research topic on DNA transformation is sorting by reversal. Here one calculates distances between genomes in terms of the number of reversal operations necessary to transform one into the other. A crucial notion to calculate these distances is the breakpoint graph. The breakpoint graph represents both the current state and the desired state of the genome after reversal operations have been taken place.
In this talk we will consider how the notion of breakpoint graph can be introduced into the formal models of gene assembly. In this way the breakpoint graph represents both the current state of a gene, its micronuclear form, and the desired state of that gene, its macronuclear form. We will show that this notion is fruitful for gene assembly by giving a few results.