Natural Computing

, Volume 5, Issue 2, pp 203–223 | Cite as

Parallelism in Gene Assembly

  • Tero Harju
  • Chang Li
  • Ion Petre
  • Grzegorz Rozenberg
Article

Abstract

The process of gene assembly in ciliates, an ancient group of organisms, is one of the most complex instances of DNA manipulation known in any organisms. This process is fascinating from the computational point of view, with ciliates even using the linked lists data structure. Three molecular operations (ld, hi, and dlad) have been postulated for the gene assembly process. We initiate here the study of parallelism in this process, raising several natural questions, such as: when can a number of operations be applied in parallel to a gene pattern; or how many steps are needed to assemble (in parallel) a micronuclear gene. In particular, this gives rise to a new measure of complexity for the process of gene assembly in ciliates.

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Copyright information

© Springer 2006

Authors and Affiliations

  • Tero Harju
    • 1
  • Chang Li
    • 2
  • Ion Petre
    • 3
  • Grzegorz Rozenberg
    • 4
    • 5
  1. 1.Department of MathematicsUniversity of Turku, Turku Center for Computer ScienceTurkuFinland
  2. 2.Department of Computer ScienceÅbo Akademi University, Turku Center for Computer ScienceTurkuFinland
  3. 3.Academy of Finland and Department of Computer ScienceÅbo Akademi University, Turku Center for Computer ScienceTurkuFinland
  4. 4.Leiden Institute for Advanced Computer ScienceLeiden UniversityLeidenThe Netherlands
  5. 5.Department of Computer ScienceUniversity of ColoradoBoulderUSA

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