There has been much interest in characterizing the DNA rearrangment capacity of ciliates both for a better general understanding of the biological processes involved and for the purposes of molecular computing. Much of the work describing the formal language theoretic aspects of ciliate DNA rearrangment has been focused on closure properties of proposed models or solutions to specific computational problems using one of the formal models.

In this talk, I will describe template-guided recombination (TGR), one model for ciliate DNA rearrangment which has received a significant amount of attention recently. I will describe recent results which are motivated by viewing the ciliate as a programmable device. The results deal with equivalence and minimality of different instances of TGR. No knowledge of biology is assumed.