Advertisement

New Generation Computing

, Volume 20, Issue 3, pp 279–293 | Cite as

On some operations on strings suggested by gene assembly in ciliates

  • Rudolf Freund
  • Carlos Martín-Vide
  • Victor Mitrana
Special Issue

Abstract

We define three operations on strings and languages suggested by the process of gene assembly in hypotrichous ciliates. This process is considered to be a prine example of DNA computing in vivo. This paper is devoted to some computational aspects of these operations from a formal language point of view. The closure of the classes of regular and context-free languages under these operations is settled. Then, we consider theld-macronuclear language of a given languageL, which consists of allld-macronuclear strings obtained from the strings ofL by iteratively applying the loop-direct repeat-excision. Finally, we discuss some open problems and further directions of research.

Keywords

Molecular Computing gac-Scheme Macronuclear String 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1).
    Dassow, J. and Mitrana, V., “On Some Operations Suggested by Genome Evolution,”in Proc. of Second Pacific Symposium on Biocomputing (Altman, R. B., Dunker, A. K., Hunter, L. and Klein, T., eds.), World Scientific, pp. 97–108, 1997.Google Scholar
  2. 2).
    Dassow, J. and Pâun, Gh., “Remarks on Operations Suggested by Mutations in Genomes,”Fundam. Inform. 36, pp. 183–200, 1998.MathSciNetzbMATHGoogle Scholar
  3. 3).
    Dassow, J., Mitrana, V. and Salomaa, A., “Context-free Evolutionary Grammars and the Structural Language of Nucleic Acids,”BioSystems, 43, pp. 169–177, 1997.CrossRefGoogle Scholar
  4. 4).
    Ehrenfeucht, A., Prescott, D. M. and Rozenberg, G., “Computational Aspects of Gene (un)Scrambling in Cilitates,”in Evolution as Computation (Landweber, L. and Winfree, E., eds.), Springer Verlag, Berlin, pp. 45–86, 2001.Google Scholar
  5. 5).
    Ehrenfeucht, A., Petre, I, Prescott, D. M. and Rozenberg, G., “Universal and Simple Operations for Gene Assembly in Ciliates,”in Where Mathematics, Computer Science, Linguistics and Biology Meet (Martín-Vide, C. and Mitrana, V., eds.), Kluwer Academic, Dordrecht, pp. 329–343, 2000.Google Scholar
  6. 6).
    Ehrenfeucht, A., Harju, T., Petre, I. and Rozenberg, G., “Patterns of Micronuclear Genes in Ciliates,”in Proc. of the 7th DIMACS meeting on DNA based computers, Tampa, Florida, pp. 33–42, 2001.Google Scholar
  7. 7).
    Knuth, D. E., Morris, J. H. and Pratt, V. R., “Fast Pattern Matching in Strings,”SIAM J. Comput., 6, pp. 323–350, 1977.MathSciNetCrossRefGoogle Scholar
  8. 8).
    Landweber, L. F. and Kari, L., “The Evolution of Cellular Computing: Nature's Solution to a Computational Problem,”in Proc. of the 4th Meeting on DNA Based Computers. BioSystems (special issue) 52, pp. 3–13, 1999.CrossRefGoogle Scholar
  9. 9).
    Landweber, L. F. and Kari, L., “Universal Molecular Computation in Ciliates,” to appear inEvolution as Computation (Landweber, L. and Winfree, E., eds.), Springer Verlag, Berlin.Google Scholar
  10. 10).
    Prescott, D. M., “Genome Gymnastics: Unique Modes of DNA Evolution and Processing in Ciliates,”Nature Reviews Genetics, 1, 3, pp. 191–198, 2000.CrossRefGoogle Scholar
  11. 11).
    Handbook of Formal Languages, 3 (Rozenberg, G. and Salomaa, A., eds.), Springer-Verlag, Berlin, 1997.zbMATHGoogle Scholar
  12. 12).
    Searls, D. B., “The Computational Linguistics of Biological Sequences,”Artificial Intelligence and Molecular Biology (Hunter, L., ed.), AAAI Press, The MIT Press, pp. 47–120, 1993.Google Scholar
  13. 13).
    Therman, E. and Susman, M.,Human Chromosomes, Structure, Behavior, and Effects, Springer-Verlag, 1993.CrossRefGoogle Scholar
  14. 14).
    Yokomori, T. and Kobayashi, S., “DNA Evolutionary Linguistics and RNA Structure Modelling: a Computational Approach,”in IEEE Symp. on Intelligence in Neural and Biological Systems, IEEE Computer Society Press, pp. 38–45, 1995.Google Scholar

Copyright information

© Ohmsha, Ltd. and Springer 2002

Authors and Affiliations

  • Rudolf Freund
    • 1
  • Carlos Martín-Vide
    • 2
  • Victor Mitrana
    • 3
  1. 1.Institute of Computer LanguagesVienna University of TechnologyWienAustria
  2. 2.Research Group in Mathematical LinguisticsRovira i Virgili UniversityTarragonaSpain
  3. 3.Faculty of MathematicsUniversity of BucharestBucharestRomania

Personalised recommendations