Two models for gene assembly in ciliates

Abstract. Two models for gene assembly in ciliates have been proposed and investigated in the last few years. The DNA manipulations postu-lated in the two models are very different: one model is intramolecular – a single DNA molecule is involved here, folding on itself according to various patterns, while the other is intermolecular – two DNA molecules may be involved here, hybridizing with each other. Consequently, the assembly strategies predicted by the two models are completely differ-ent. Interestingly however, the final result of the assembly (including the assembled gene) is always the same. We compare in this paper the two models for gene assembly, formalizing both in terms of pointer reductions. We also discuss invariants and universality results for both models.