String and graph reduction systems for gene assembly in ciliates

Authors:
Andrzej Ehrenfeucht;Ion Petre;David M. Prescott;Grzegorz Rozenberg
Affiliations:
University of Colorado, Department of Computer Science, Boulder CO 80309-0347 USA/ Email: andrzej@cs.colorado.edu;Turku Centre for Computer Science and Department of Mathematics, University of Turku, FIN 20520, Finland/ Email: ipetre@cs.utu.fi;University of Colorado, Department of Molecular, Cellular and Developmental Biology, Boulder CO 80309-0347 USA/ Email: prescotd@spot.colorado.edu;Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333 CA Leiden, The Netherlands and University of Colorado, Department of Molecular, Cellular and Developmental B ...
Venue:
Mathematical Structures in Computer Science
Year:
2002

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Abstract

Ciliates have developed a unique nuclear dualism, having two nuclei of different functionality: the germline micronucleus and the somatic macronucleus. The way that ciliates assemble the macronuclear genes after cell mating constitutes one of the most intricate DNA processings in living organisms. This processing is also very interesting from the computational point of view. In this paper, we investigate the operations of loop excision and hairpin excision/reinsertion used in the assembly process. In particular, we consider three levels of formalization of this process, culminating in graph reduction systems.