Formal systems for gene assembly in ciliates

DNA processing in ciliates, a very ancient group of organisms, is among the most sophisticated DNA processing in living organisms. It has a quite clear computational structure and even uses explicitly the linked list data structure! Particularly interesting from the computational point of view is the process of gene assembly from its micronuclear to its macronuclear form. We investigate here the string rewriting and the graph rewriting models of this process, involving three molecular operations, which together form a universal set of operations in the sense that they can assembly any macronuclear gene from its micronuclear form. In particular we prove that although the graph rewriting system is more "abstract" than the string rewriting system, no "essential information" is lost, in the sense that one can translate assembly strategies from one system into the other.