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Parallelism in Gene Assembly

  • Tero Harju
  • Chang Li
  • Ion Petre
  • Grzegorz Rozenberg
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3384)

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 list data structure. Three molecular operations (ld,hi, and dlad) have been postulated for the gene assembly process. We initiate here the study of parallelism of this process by investigating 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. We believe that the study of parallelism contributes to a better understanding of the nature of gene assembly, and in particular it provides a new insight in the complexity of this process.

Keywords

Gene Assembly Parallel Strategy Signed Graph Parallel Complexity Ciliated Protozoan 
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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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Tero Harju
    • 1
    • 3
  • Chang Li
    • 2
    • 3
  • Ion Petre
    • 2
    • 3
  • Grzegorz Rozenberg
    • 4
    • 5
  1. 1.Department of MathematicsUniversity of TurkuTurkuFinland
  2. 2.Department of Computer ScienceÅbo Akademi UniversityTurkuFinland
  3. 3.Turku Centre for Computer ScienceTurkuFinland
  4. 4.Leiden Institute for Advanced Computer ScienceLeiden UniversityLeidenThe Netherlands
  5. 5.Department of Computer ScienceUniversity of Colorado at BoulderBoulderUSA

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