Computational Processes in Living Cells: Gene Assembly in Ciliates

  • Tero Harju
  • Grzegorz Rozenberg
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2450)


One of the most complex DNA processing in nature known to us is carried out by ciliates during the sexual reproduction when their micronuclear genome is transformed to the macronuclear genome. This process of gene assembly is intriguing and captivating also from the computational point of view. We investigate here three intramolecular molecular operations (ld, hi, and dlad) postulated to accomplish gene assembly. The formal models for these operations are formulated on three different abstraction levels: MDS descriptors, legals strings and overlap graphs. In general both legal strings and overlap graphs contain strings and graphs that do not model any micronuclear gene. After a short survey of gene assembly we study the problem of recognizing whether a general legal string or a general overlap graph is a formalization of a micronuclear gene.


Lution Boulder 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Tero Harju
    • 1
  • Grzegorz Rozenberg
    • 2
    • 3
  1. 1.Department of MathematicsUniversity of TurkuTurkuFinland
  2. 2.Leiden Institute for Advanced Computer ScienceLeiden UniversityCA Leidenthe Netherlands
  3. 3.Department of Computer ScienceUniversity of Colorado at BoulderBoulderUSA

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