On Computational Processes Performed during the Gene Assembly in Ciliates

Ciliates are protozoic single-celled organisms widely studied due to their nuclear dualism property, that is they have two tapes of nuclei, a micronucleus (to store the DNA) and a macronucleus (to provide the RNA). Another feature that makes them distinct is the phenomenon of transformation of micronuclear genes into macronuclear genes, during their reproduction, known in literature as gene assembly process in ciliates. This process is based on three molecular operations: ld (loop, direct repeat), hi (hairpin, inverted repeat) and dlad (double loop, alternating direct repeat). In this paper we focus on the mathematical formalization and generalization of these operations.