On codes defined by bio-operations

Authors:
Mark Daley;Michael Domaratzki
Affiliations:
Departments of Computer Science and Biology, University of Western Ontario, London, ON N6A 5B7, Canada;Department of Computer Science, University of Manitoba, Winnipeg, MB R3T 2T2, Canada
Venue:
Theoretical Computer Science
Year:
2007

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Abstract

We consider the classes of @?-codes and @?-codes, which are superclasses of outfix and hyper-codes, respectively. These restrictions are based on the synchronized insertion operation, which serves as a model for the gene rearrangement function in certain unicellular organisms. We investigate the classes of @?-codes and @?-codes from a theoretical perspective, examine their relationships with traditional code classes and consider related decidability problems.