Formal Properties of Gene Assembly: Equivalence Problem for Overlap Graphs

  • Tero Harju
  • Ion Petre
  • Grzegorz Rozenberg
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2950)


Gene assembly in ciliates is a life process fascinating from both the biological and the computational points of view. Several formal models of this process have been formulated and investigated, among them a model based on (legal) strings and a model based on (overlap) graphs. The latter is more abstract because the translation of legal strings into overlap graphs is not injective. In this paper we consider and solve the overlap equivalence problem for realistic strings: when do two different realistic legal strings translate into the same overlap graph? Realistic legal strings are legal strings that “really” correspond to genes generated during the gene assembly process.


Formal Property Equivalence Problem Gene Assembly Signed Graph Circle Graph 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Tero Harju
    • 1
  • Ion Petre
    • 2
  • Grzegorz Rozenberg
    • 3
    • 4
  1. 1.Department of MathematicsUniversity of TurkuTurkuFinland
  2. 2.Department of Computer ScienceÅbo Akademi UniversityTurkuFinland
  3. 3.Leiden Institute for Advanced Computer ScienceLeiden UniversityLeidenthe Netherlands
  4. 4.Department of Computer ScienceUniversity of ColoradoBoulderUSA

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