Template-guided DNA recombination

The family of stichotrichous ciliates have received a great deal of study due to the presence of scrambled genes in their genomes. The mechanism by which these genes are descrambled is of interest both as a biological process and as a model of natural computation. Several formal models of this process have been proposed, the most recent of which involves the recombination of DNA strands based on template guides. We generalize this template-guided DNA recombination model proposed by Prescott, Ehrenfeucht and Rozenberg to an operation on strings and languages. We then proceed to investigate the properties of this operation with the intention of viewing ciliate gene descrambling as a computational process.