Skip to main content
Springer Nature Link
Log in

Simple Operations for Gene Assembly

  • Conference paper
DNA Computing (DNA 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3892))

Included in the following conference series:

  • 803 Accesses

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  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. 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. 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)

    Article  MathSciNet  MATH  Google Scholar 

  4. Ehrenfeucht, A., Harju, T., Petre, I., Rozenberg, G.: Characterizing the micronuclear gene patterns in ciliates. Theory of Comput. Syst. 35, 501–519 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  5. Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., Rozenberg, G.: Computation in Living Cells: Gene Assembly in Ciliates. Springer, Heidelberg (2003)

    MATH  Google Scholar 

  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)

    Chapter  Google Scholar 

  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)

    MathSciNet  MATH  Google Scholar 

  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)

    Chapter  Google Scholar 

  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. 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. 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. 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. 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. 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. Jahn, C.L., Klobutcher, L.A.: Genome remodeilng in ciliated protozoa. Ann. Rev. Microbiol. 56, 489–520 (2000)

    Article  Google Scholar 

  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)

    Article  MathSciNet  MATH  Google Scholar 

  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. 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. Landweber, L.F., Kari, L.: Universal molecular computation in ciliates. In: Landweber, L.F., Winfree, E. (eds.) Evolution as Computation. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  20. Prescott, D.M.: Cells: Principles of Molecular Structure and Function. Jones and Barlett, Boston (1988)

    Google Scholar 

  21. Prescott, D.M.: Cutting, splicing, reordering, and elimination of DNA sequences in hypotrichous ciliates. BioEssays 14, 317–324 (1992)

    Article  Google Scholar 

  22. Prescott, D.M.: The unusual organization and processing of genomic DNA in hypotrichous ciliates. Trends in Genet. 8, 439–445 (1992)

    Article  Google Scholar 

  23. Prescott, D.M.: The DNA of ciliated protozoa. Microbiol. Rev. 58(2), 233–267 (1994)

    MathSciNet  Google Scholar 

  24. Prescott, D.M.: The evolutionary scrambling and developmental unscabling of germlike genes in hypotrichous ciliates. Nucl. Acids Res. 27, 1243–1250 (1999)

    Article  Google Scholar 

  25. Prescott, D.M.: Genome gymnastics: Unique modes of DNA evolution and processing in ciliates. Nat. Rev. Genet. 1(3), 191–198 (2000)

    Article  Google Scholar 

  26. Prescott, D.M., DuBois, M.: Internal eliminated segments (IESs) of Oxytrichidae. J. Eukariot. Microbiol. 43, 432–441 (1996)

    Article  Google Scholar 

  27. Prescott, D.M., Ehrenfeucht, A., Rozenberg, G.: Molecular operations for DNA processing in hypotrichous ciliates. Europ. J. Protistology 37, 241–260 (2001)

    Article  Google Scholar 

  28. Prescott, D.M., Rozenberg, G.: How ciliates manipulate their own DNA - A splendid example of natural computing. Natural Computing 1, 165–183 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  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 

Download references

Author information

Authors and Affiliations

  1. Department of Mathematics, University of Turku, Turku, 20014, Finland

    Tero Harju

  2. Academy of Finland, Finland

    Ion Petre

  3. Department of Computer Science, Åbo Akademi University, Turku, 20520, Finland

    Ion Petre & Vladimir Rogojin

  4. Turku Centre for Computer Science, Turku, 20520, Finland

    Tero Harju, Ion Petre & Vladimir Rogojin

  5. Leiden Institute for Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333 CA, Leiden, The Netherlands

    Grzegorz Rozenberg

  6. Department of Computer Science, University of Colorado at Boulder, Boulder, Co, 80309-0347, USA

    Grzegorz Rozenberg

Authors
  1. Tero Harju
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ion Petre
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Vladimir Rogojin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Grzegorz Rozenberg
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Computer Science, Université Pierre et Marie Curie, INSERM U511,, 91 Boulevard de L’Hôpital, 75013, Paris, France

    Alessandra Carbone

  2. California Institute of Technology, Applied and Computational Mathematics, Bioengineering,, MC 114-96, 91125, Pasadena, CA, USA

    Niles A. Pierce

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Harju, T., Petre, I., Rogojin, V., Rozenberg, G. (2006). Simple Operations for Gene Assembly. In: Carbone, A., Pierce, N.A. (eds) DNA Computing. DNA 2005. Lecture Notes in Computer Science, vol 3892. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11753681_8

Download citation

  • DOI: https://doi.org/10.1007/11753681_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-34161-1

  • Online ISBN: 978-3-540-34165-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics