Formal systems for gene assembly in ciliates

  • Authors:

  • Andrzej Ehrenfeucht;Tero Harju;Ion Petre;David M. Prescott;Grzegorz Rozenberg

  • Affiliations:

  • Department of Computer Science, University of Colorado, Boulder, CO;Department of Mathematics, University of Turku, FIN 20014, Turku, Finland;Turku Centre for Computer Science, FIN 20520, Turku, Finland and Department of Mathematics, University of Turku, FIN 20014, Turku, Finland;Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO;Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333 CA Leiden, Netherlands and Department of Computer Science, University of Colorado, Boulder, CO

  • Venue:
  • Theoretical Computer Science
  • Year:
  • 2003

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Abstract

DNA processing in ciliates, a very ancient group of organisms, is among the most sophisticated DNA processing in living organisms. It has a quite clear computational structure and even uses explicitly the linked list data structure! Particularly interesting from the computational point of view is the process of gene assembly from its micronuclear to its macronuclear form. We investigate here the string rewriting and the graph rewriting models of this process, involving three molecular operations, which together form a universal set of operations in the sense that they can assembly any macronuclear gene from its micronuclear form. In particular we prove that although the graph rewriting system is more "abstract" than the string rewriting system, no "essential information" is lost, in the sense that one can translate assembly strategies from one system into the other.