Simple Operations for Gene Assembly

  • Tero Harju
  • Ion Petre
  • Vladimir Rogojin
  • Grzegorz Rozenberg
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3892)

Abstract

The intramolecular model for gene assembly in ciliates considers three operations, ld, hi, and dlad that can assemble any gene pattern through folding and recombination: the molecule is folded so that two occurrences of a pointer (short nucleotide sequence) get aligned and then the sequence is rearranged through recombination of pointers. In general, the sequence rearranged by one operation can be arbitrarily long and consist of many coding and non-coding blocks. We consider in this paper some simpler variants of the three operations, where only one coding block is rearranged at a time. We characterize in this paper the gene patterns that can be assembled through these variants. Our characterization is in terms of signed permutations and dependency graphs. Interestingly, we show that simple assemblies possess rather involved properties: a gene pattern may have both successful and unsuccessful assemblies and also more than one successful assembling strategy.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Berman, P., Hannenhalli, S.: Fast sorting by reversals. In: Kasturi, R., Tombre, K. (eds.) Graphics Recognition 1995. LNCS, vol. 1072, pp. 168–185. Springer, Heidelberg (1996)Google Scholar
  2. 2.
    Caprara, A.: Sorting by reversals is difficult. In: Istrail, S., Pevzner, P., Waterman, M. (eds.) Proceedings of the 1st Annual International Conference on Computational Molecular Biology, pp. 75–83 (1997)Google Scholar
  3. 3.
    Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., Rozenberg, G.: Formal systems for gene assembly in ciliates. Theoret. Comput. Sci. 292, 199–219 (2003)MathSciNetCrossRefMATHGoogle Scholar
  4. 4.
    Ehrenfeucht, A., Harju, T., Petre, I., Rozenberg, G.: Characterizing the micronuclear gene patterns in ciliates. Theory of Comput. Syst. 35, 501–519 (2002)MathSciNetCrossRefMATHGoogle Scholar
  5. 5.
    Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., Rozenberg, G.: Computation in Living Cells: Gene Assembly in Ciliates. Springer, Heidelberg (2003)MATHGoogle Scholar
  6. 6.
    Ehrenfeucht, A., Petre, I., Prescott, D.M., Rozenberg, G.: Universal and simple operations for gene assembly in ciliates. In: Mitrana, V., Martin-Vide, C. (eds.) Words, Sequences, Languages: Where Computer Science, Biology and Linguistics Meet, pp. 329–342. Kluwer Academic, Dortrecht (2001)CrossRefGoogle Scholar
  7. 7.
    Ehrenfeucht, A., Petre, I., Prescott, D.M., Rozenberg, G.: String and graph reduction systems for gene assembly in ciliates. Math. Structures Comput. Sci. 12, 113–134 (2001)MathSciNetMATHGoogle Scholar
  8. 8.
    Ehrenfeucht, A., Petre, I., Prescott, D.M., Rozenberg, G.: Circularity and other invariants of gene assembly in cliates. In: Ito, M., Păun, G., Yu, S. (eds.) Words, semigroups, and transductions, pp. 81–97. World Scientific, Singapore (2001)CrossRefGoogle Scholar
  9. 9.
    Ehrenfeucht, A., Prescott, D.M., Rozenberg, G.: Computational aspects of gene (un)scrambling in ciliates. In: Landweber, L.F., Winfree, E. (eds.) Evolution as Computation, pp. 216–256. Springer, Heidelberg (2001)Google Scholar
  10. 10.
    Hannenhalli, S., Pevzner, P.A.: Transforming cabbage into turnip (Polynomial algorithm for sorting signed permutations by reversals). In: Proceedings of the 27th Annual ACM Symposium on Theory of Computing, pp. 178–189 (1995)Google Scholar
  11. 11.
    Harju, T., Petre, I., Li, C., Rozenberg, G.: Parallelism in gene assembly. In: Proceedings of DNA-based computers 10. Springer, Heidelberg (to appear, 2005)Google Scholar
  12. 12.
    Harju, T., Petre, I., Rozenberg, G.: Gene assembly in ciliates: Molecular operations. In: Paun, G., Rozenberg, G., Salomaa, A. (eds.) Current Trends in Theoretical Computer Science (2004)Google Scholar
  13. 13.
    Harju, T., Petre, I., Rozenberg, G.: Gene assembly in ciliates: Formal frameworks. In: Paun, G., Rozenberg, G., Salomaa, A. (eds.) Current Trends in Theoretical Computer Science (2004)Google Scholar
  14. 14.
    Harju, T., Petre, I., Rozenberg, G.: Modelling simple operations for gene assembly (submitted, 2005); Also as a TUCS technical report TR697, http://www.tucs.fi
  15. 15.
    Jahn, C.L., Klobutcher, L.A.: Genome remodeilng in ciliated protozoa. Ann. Rev. Microbiol. 56, 489–520 (2000)CrossRefGoogle Scholar
  16. 16.
    Kaplan, H., Shamir, R., Tarjan, R.E.: A faster and simpler algorithm for sorting signed permutations by reversals. SIAM J. Comput. 29, 880–892 (1999)MathSciNetCrossRefMATHGoogle Scholar
  17. 17.
    Kari, L., Landweber, L.F.: Computational power of gene rearrangement. In: Winfree, E., Gifford, D.K. (eds.) Proceedings of DNA Bases Computers, V, pp. 207–216. American Mathematical Society (1999)Google Scholar
  18. 18.
    Landweber, L.F., Kari, L.: The evolution of cellular computing: Nature’s solution to a computational problem. In: Proceedings of the 4th DIMACS Meeting on DNA-Based Computers, Philadelphia, PA, pp. 3–15 (1998)Google Scholar
  19. 19.
    Landweber, L.F., Kari, L.: Universal molecular computation in ciliates. In: Landweber, L.F., Winfree, E. (eds.) Evolution as Computation. Springer, Heidelberg (2002)CrossRefGoogle Scholar
  20. 20.
    Prescott, D.M.: Cells: Principles of Molecular Structure and Function. Jones and Barlett, Boston (1988)Google Scholar
  21. 21.
    Prescott, D.M.: Cutting, splicing, reordering, and elimination of DNA sequences in hypotrichous ciliates. BioEssays 14, 317–324 (1992)CrossRefGoogle Scholar
  22. 22.
    Prescott, D.M.: The unusual organization and processing of genomic DNA in hypotrichous ciliates. Trends in Genet. 8, 439–445 (1992)CrossRefGoogle Scholar
  23. 23.
    Prescott, D.M.: The DNA of ciliated protozoa. Microbiol. Rev. 58(2), 233–267 (1994)MathSciNetGoogle Scholar
  24. 24.
    Prescott, D.M.: The evolutionary scrambling and developmental unscabling of germlike genes in hypotrichous ciliates. Nucl. Acids Res. 27, 1243–1250 (1999)CrossRefGoogle Scholar
  25. 25.
    Prescott, D.M.: Genome gymnastics: Unique modes of DNA evolution and processing in ciliates. Nat. Rev. Genet. 1(3), 191–198 (2000)CrossRefGoogle Scholar
  26. 26.
    Prescott, D.M., DuBois, M.: Internal eliminated segments (IESs) of Oxytrichidae. J. Eukariot. Microbiol. 43, 432–441 (1996)CrossRefGoogle Scholar
  27. 27.
    Prescott, D.M., Ehrenfeucht, A., Rozenberg, G.: Molecular operations for DNA processing in hypotrichous ciliates. Europ. J. Protistology 37, 241–260 (2001)CrossRefGoogle Scholar
  28. 28.
    Prescott, D.M., Rozenberg, G.: How ciliates manipulate their own DNA - A splendid example of natural computing. Natural Computing 1, 165–183 (2002)MathSciNetCrossRefMATHGoogle Scholar
  29. 29.
    Prescott, D.M., Rozenberg, G.: Encrypted genes and their reassembly in ciliates. In: Amos, M. (ed.) Cellular Computing. Oxford University Press, Oxford (2003)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Tero Harju
    • 1
    • 4
  • Ion Petre
    • 2
    • 3
    • 4
  • Vladimir Rogojin
    • 3
    • 4
  • Grzegorz Rozenberg
    • 5
    • 6
  1. 1.Department of MathematicsUniversity of TurkuTurkuFinland
  2. 2.Academy of FinlandFinland
  3. 3.Department of Computer ScienceÅbo Akademi UniversityTurkuFinland
  4. 4.Turku Centre for Computer ScienceTurkuFinland
  5. 5.Leiden Institute for Advanced Computer ScienceLeiden UniversityLeidenThe Netherlands
  6. 6.Department of Computer ScienceUniversity of Colorado at BoulderBoulderUSA

Personalised recommendations