Ciliates have developed a unique nuclear dualism, having two nuclei of different functionality: the germline micronucleus and the somatic macronucleus. The way that ciliates assemble the macronuclear genes after cell mating constitutes one of the most intricate DNA processings in living organisms. This processing is also very interesting from the computational point of view. In this paper, we investigate the operations of loop excision and hairpin excision/reinsertion used in the assembly process. In particular, we consider three levels of formalization of this process, culminating in graph reduction systems.