Patterns of Micronuclear Genes in Ciliates

  • Andrzej Ehrenfeucht
  • Tero Harju
  • Ion Petre
  • Grzegorz Rozenberg
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2340)

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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References

  1. 1.
    Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., and Rozenberg, G., Formal systems for gene assembly in ciliates, to appear in Theoret. Comput. Sci. (2001).Google Scholar
  2. 2.
    Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., and Rozenberg, G., Patterns of micronuclear genes in ciliates, manuscript.Google Scholar
  3. 3.
    Ehrenfeucht, A., Petre, I., Prescott, D. M., and Rozenberg, G., Universal and simple operations for gene assembly in ciliates, in C. Martin-Vide and V. Mitrana (eds.) Where Mathematics, Computer Science, Linguistics and Biology Meet, Kluwer Academic Publishers, Dordrecht/Boston, 329–342 (2001).Google Scholar
  4. 4.
    Ehrenfeucht, A., Petre, I., Prescott, D.M., and Rozenberg, G., String and graph reduction systems for gene assembly in ciliates, to appear in Math. Struct. in Comput. Sci. (2001).Google Scholar
  5. 5.
    Ehrenfeucht, A., Petre, I., Prescott, D.M., and Rozenberg, G., Circular gene assembly in ciliates, manuscript (2001).Google Scholar
  6. 6.
    Ehrenfeucht, A., Prescott, D.M., and Rozenberg, G., Computational aspects of gene (un)scrambling in ciliates. In Evolution as Computation, L. Landweber and E. Winfree (eds.), 45–86, Springer Verlag, Berlin, Heidelberg (2001).Google Scholar
  7. 7.
    Landweber, L.F. and Kari, L., The evolution of cellular computing: nature’s solution to a computational problem. Proceedings of the 4th DIMACS meeting on DNA based computers, Philadelphia, 3–15 (1998).Google Scholar
  8. 8.
    Landweber, L.F. and Kari, L., Universal molecular computation in ciliates. In Evolution as Computation, Landweber, L. and Winfree, E. (eds.), Springer Verlag, Berlin, Heidelberg, to appear (1999).Google Scholar
  9. 9.
    Prescott, D.M., Cutting, splicing, reordering, and elimination of DNA sequences in Hypotrichous ciliates. BioEssays, 14(5): 317–324 (1992).CrossRefGoogle Scholar
  10. 10.
    Prescott, D.M., The unusual organization and processing of genomic DNA in Hypotrichous ciliates. Trends in Genet. 8:439–445 (1992).Google Scholar
  11. 11.
    Prescott, D.M. and DuBois, M., Internal eliminated segments (IESs) of Oxytrichidae, J. Eukariot. Microbiol. 43, 432–441 (1996).CrossRefGoogle Scholar
  12. 12.
    Prescott, D.M., Ehrenfeucht, A., and Rozenberg, G., Molecular operations for DNA processing in Hypotrichous ciliates, to appear in European Journal of Protistology (2001).Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2002

Authors and Affiliations

  • Andrzej Ehrenfeucht
    • 1
  • Tero Harju
    • 2
    • 3
  • Ion Petre
    • 2
    • 3
  • Grzegorz Rozenberg
    • 1
    • 4
  1. 1.Department of Computer ScienceUniversity of ColoradoBoulderUSA
  2. 2.Department of MathematicsUniversity of TurkuFinland
  3. 3.Turku Centre for Computer ScienceTurkuFinland
  4. 4.Leiden Institute of Advanced Computer ScienceLeiden UniversityLeidenThe Netherlands

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