Theory of Computing Systems

, Volume 35, Issue 5, pp 501–519 | Cite as

Characterizing the Micronuclear Gene Patterns in Ciliates

  • Andrzej Ehrenfeucht
  • Tero Harju
  • Ion Petre
  • Grzegorz Rozenberg
Article

Abstract

The process of gene assembly in ciliates is one of the most complex examples of DNA processing known in any organism, and it is fascinating from the computational point of view—it is a prime example of DNA computing in vivo. In this paper we continue to investigate the three molecular operations (ld, hi , and dlad ) that were postulated to carry out the gene assembly process in the intramolecular fashion. In particular, we focus on the understanding of the IES/ MDS patterns of micronuclear genes, which is one of the important goals of research on gene assembly in ciliates. We succeed in characterizing for each subset S of the three molecular operations those patterns that can be assembled using operations in S. These results enhance our understanding of the structure of micronuclear genes (and of the nature of molecular operations). They allow one to establish both similarity and complexity measures for micronuclear genes.

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Copyright information

© Springer-Verlag New York 2002

Authors and Affiliations

  • Andrzej Ehrenfeucht
    • 1
  • Tero Harju
    • 2
  • Ion Petre
    • 3
  • Grzegorz Rozenberg
    • 1
  1. 1.Department of Computer Science, University of Colorado, andrzej@cs.colorado.eduBoulderUSA
  2. 2.Department of Mathematics, University of Turku and Turku Centre for Computer Science, harju@utu.fiFinland
  3. 3.Turku Centre for Computer Science and Department of Mathematics, University of Turku, ipetre@cs.utu.fiTurkuFinland
  4. 4.Leiden Institute of Advanced Computer Science, Leiden University, rozenber@liacs.nlLeidenThe Netherlands

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