Complexity Measures for Gene Assembly

  • Tero Harju
  • Chang Li
  • Ion Petre
  • Grzegorz Rozenberg
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4366)


The process of gene assembly in ciliates is a fascinating example of programmed DNA manipulations in living cells. Macronuclear genes are split into coding blocks (called MDSs), shuffled and separated by non-coding sequences to form micronuclear genes. Assembling the coding blocks from micronuclear genes to form functional macronuclear genes is facilitated by an impressive in-vivo implementation of the linked list data structure of computer science. Complexity measures for genes may be defined in many ways, including the number of MDSs, the number of loci, etc. We take a different approach in this paper and propose four complexity measures for genes in ciliates, based on the ‘effort’ required to assemble the gene. We consider: (a) the types of operations used in the assembly, (b) the number of operations used in the assembly, (c) the length of the molecular folds involved, and (d) the length of the shortest possible parallel assembly for that gene.

“One of the oldest forms of life on Earth has been revealed as a natural born computer programmer.”

BBC, September 10, 2001.


Reduction Strategy Complexity Measure Gene Assembly Signed Graph Parallel Complexity 
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  1. 1.
    Brijder, R., Hoogeboom, H.J., Rozenberg, G.: Reducibility of gene patterns in cliates using the breakpoint graph. To appear in Theoret. Comput. Sci. (2006)Google Scholar
  2. 2.
    Cavalcanti, A., Clarke, T.H., Landweber, L.: MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates. Nucleic Acids Research 33, 396–398 (2005)CrossRefGoogle Scholar
  3. 3.
    Chang, W.J., et al.: The evolutionary origin of a complex scrambled gene. Proceedings of the National Academy of Sciences of the US 102(42), 15149–15154 (2005)CrossRefGoogle Scholar
  4. 4.
    Chang, W.J., Kuo, S., Landweber, L.: A new scrambled gene in the ciliate Uroleptus. Gene, to appear (2006)Google Scholar
  5. 5.
    Ehrenfeucht, A., et al.: Characterizing the micronuclear gene patterns in ciliates. Theory of Comput. Syst. 35, 501–519 (2002)MATHCrossRefMathSciNetGoogle Scholar
  6. 6.
    Ehrenfeucht, A., et al.: Computation in Living Cells: Gene Assembly in Ciliates. Springer, Heidelberg (2004)MATHGoogle Scholar
  7. 7.
    Ehrenfeucht, A., et al.: 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)Google Scholar
  8. 8.
    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
  9. 9.
    Harju, T., Li, C., Petre, I.: Results on parallel reductions of signed overlap graphs. Manuscript (2006)Google Scholar
  10. 10.
    Harju, T., et al.: Simple operations for gene assembly. In: Carbone, A., Pierce, N.A. (eds.) DNA Computing. LNCS, vol. 3892, pp. 96–111. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  11. 11.
    Harju, T., Petre, I., Rozenberg, G.: Modelling simple operations for gene assembly. In: Chen, J., Jonoska, N., Rozenberg, G. (eds.) Nanotechnology: Science and Computation, pp. 361–376 (2006)Google Scholar
  12. 12.
    Jahn, C.L., Klobutcher, L.A.: Genome remodeling in ciliated protozoa. Ann. Rev. Microbiol. 56, 489–520 (2000)CrossRefGoogle Scholar
  13. 13.
    Langille, M., Petre, I.: Simple gene assembly is deterministic. Fundamenta Informaticae. IOS Press, Amsterdam (2006)Google Scholar
  14. 14.
    Harju, T., et al.: Simple operations for gene assembly. In: Carbone, A., Pierce, N.A. (eds.) DNA Computing. LNCS, vol. 3892, Springer, Heidelberg (2006)CrossRefGoogle Scholar
  15. 15.
    Harju, T., et al.: Parallelism in gene assemby. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA Computing. LNCS, vol. 3384, pp. 140–150. Springer, Heidelberg (2005)Google Scholar
  16. 16.
    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
  17. 17.
    Landweber, L.F., Kari, L.: Universal molecular computation in ciliates. In: Landweber, L.F., Winfree, E. (eds.) Evolution as Computation, Springer, Heidelberg (2002)Google Scholar
  18. 18.
    Petre, I., Skogman, S.: Gene assembly simulator (2006),
  19. 19.
    Prescott, D.M.: The DNA of ciliated protozoa. Microbiol. Rev. 58(2), 233–267 (1994)Google Scholar
  20. 20.
    Prescott, D.M.: DNA manipulations in ciliates. In: Brauer, W., et al. (eds.) Formal and Natural Computing. LNCS, vol. 2300, pp. 394–417. Springer, Heidelberg (2002)CrossRefGoogle Scholar
  21. 21.
    Prescott, D.M., Ehrenfeucht, A., Rozenberg, G.: Molecular operations for DNA processing in hypotrichous ciliates. Europ. J. Protistology 37, 241–260 (2001)CrossRefGoogle Scholar
  22. 22.
    Swanton, M.T., Heumann, J.M., Prescott, D.M.: Gene-sized DNA molecules of the macronuclei in three species of hypotrichs: size distribution and absence of nicks. Chromosoma 77, 217–227 (1980)CrossRefGoogle Scholar
  23. 23.
    Yao, M.C., Fuller, P., Xi, X.: Programmed DNA Deletion As an RNA-Guided System of Genome Defense. Science 300, 1581–1584 (2003)CrossRefGoogle Scholar

Copyright information

© Springer Berlin Heidelberg 2007

Authors and Affiliations

  • Tero Harju
    • 1
  • Chang Li
    • 2
  • Ion Petre
    • 2
    • 3
  • Grzegorz Rozenberg
    • 4
    • 5
  1. 1.Department of Mathematics, University of Turku, Turku Center for Computer Science, FIN-20014 TurkuFinland
  2. 2.Department of Computer Science, Åbo Akademi University, Turku Center for Computer Science, FIN-20520 TurkuFinland
  3. 3.Academy of Finland 
  4. 4.Leiden Institute for Advanced Computer Science, Leiden University, 2333 CA LeidenThe Netherlands
  5. 5.Department of Computer Science, University of Colorado, Boulder, Co 80309-0347USA

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