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Molecular Operations for Gene Assembly

  • Andrzej Ehrenfeucht
  • Tero Harju
  • Ion Petre
  • David M. Prescott
  • Grzegorz Rozenberg
Part of the Natural Computing Series book series (NCS)

Abstract

We can only speculate about the significance of the extraordinary modifications in the structure of micronuclear genes in stichotrichous ciliates that have occurred during evolution. However, it is clear the presence of IESs and MDSs, and particularly the scrambling of MDSs in micronuclear genes, requires spectacular manipulations of DNA sequences whenever cells mate and then develop new macronuclei. These DNA manipulations are massive, consisting of the excision of more than 100,000 IESs and reordering of many thousands of MDSs. Major progress in understanding this intricate DNA processing has been made by studying the nucleotide sequences in micronuclear genes. The excision of IESs and the unscrambling and joining of MDSs are referred to as gene assembly. In this chapter we postulate three molecular operations based on the pairs of repeats in the ends of MDSs to accomplish the assembling of genes after cell mating. In the description of these three operations the pairs of repeats are called pointers because they point the way for MDS joining.

Keywords

Homologous Recombination Actin Gene Gene Assembly Circular Molecule Identical Segment 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Notes on References

  1. 51.
    Prescott, D. M., Ehrenfeucht, A., and Rozenberg, G., Molecular operations for DNA processing in hypotrichous ciliates. Europ. J. Protistology 37 (2001) 241–260CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Andrzej Ehrenfeucht
    • 1
  • Tero Harju
    • 2
  • Ion Petre
    • 3
  • David M. Prescott
    • 4
  • Grzegorz Rozenberg
    • 5
  1. 1.Department of Computer ScienceUniversity of ColoradoBoulderUSA
  2. 2.Department of MathematicsUniversity of TurkuTurkuFinland
  3. 3.Department of Computer ScienceÅbo Akademi UniversityTurkuFinland
  4. 4.Department of Molecular, Cellular and Developmental BiologyUniversity of ColoradoBoulderUSA
  5. 5.Leiden Institute for Advanced Computer ScienceLeiden UniversityLeidenThe Netherlands

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