Dependency relations between elementary intramolecular operations in gene assembly in ciliates

The intramolecular model of gene assembly in ciliates postulates three foldingrecombination operations over a single DNA molecule. Those operations are suggested to assemble a macronuclear contiguous gene from its shuffled and inverted micronuclear fragments. The elementary intramolecular model considers DNA rearrangements containing at most one micronuclear gene fragment. In contrast with the general model, the elementary intramolecular operations are not universal: they cannot assemble all hypothetical micronuclear gene patterns. We investigate the following general question: what micronuclear gene patterns can be assembled by elementary intramolecular operations? Currently a number of efficient solutions exists for micronuclear gene patterns without inverted gene fragments. Going towards an efficient solution for the general question, we investigate in this paper the order relation between elementary intramolecular operations within assembly strategies applicable to gene patterns with inverted fragments.