Template-guided DNA recombination

Authors:
Mark Daley;Ian McQuillan
Affiliations:
Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5A9;Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7
Venue:
Theoretical Computer Science - Descriptional complexity of formal systems
Year:
2005

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Abstract

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.