A String-Based Model for Simple Gene Assembly

  • Robert Brijder
  • Miika Langille
  • Ion Petre
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4639)


The simple intramolecular model for gene assembly in ciliates is particularly interesting because it can predict the correct assembly of all available experimental data, although it is not universal. The simple model also has a confluence property that is not shared by the general model. A previous formalization of the simple model through sorting of signed permutations is unsatisfactory because it effectively ignores one operation of the model and thus, it cannot be used to answer questions about parallelism in the model, or about measures of complexity. We propose in this paper a string-based model in which a gene is represented through its sequence of pointers and markers and its assembly is represented as a string rewriting process. We prove that this string-based model is equivalent to the permutation-based model as far as gene assembly is concerned, while it tracks all operations of the model.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Robert Brijder
    • 1
  • Miika Langille
    • 2
  • Ion Petre
    • 2
    • 3
  1. 1.Leiden Institute of Advanced Computer Science, Universiteit Leiden, Niels Bohrweg 1, 2333 CA LeidenThe Netherlands
  2. 2.Turku Centre for Computer Science, Department of IT, Åbo Akademi University, Turku 20520Finland
  3. 3.Academy ofFinland

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