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Perfect DCJ Rearrangement

  • Sèverine Bérard
  • Annie Chateau
  • Cedric Chauve
  • Christophe Paul
  • Eric Tannier
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5267)

Abstract

We study the problem of transforming a multichromosomal genome into another using Double-Cut-and-Join (DCJ) operations. We introduce the notion of DCJ scenario that does not break families of common intervals (groups of genes co-localized in both genomes). Such scenarios are called perfect, and generalize the notion of perfect reversal scenarios. While perfect sorting by reversals is NP-hard if the family of common intervals is nested, we show that finding a shortest perfect DCJ scenario can be answered in polynomial time in this case. Moreover, while perfect sorting by reversals is easy when the family of common intervals is weakly separable, we show that the corresponding problem is NP-hard in the DCJ case. These contrast with previous comparisons between the reversal and DCJ models, that showed that most problems have similar complexity in both models.

Keywords

Prime Node Common Interval Signed Permutation Breakpoint Graph Nest Family 
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 2008

Authors and Affiliations

  • Sèverine Bérard
    • 1
    • 2
  • Annie Chateau
    • 2
  • Cedric Chauve
    • 3
  • Christophe Paul
    • 2
  • Eric Tannier
    • 4
  1. 1.Université Montpellier 2, UMR AMAP, MontpellierFrance
  2. 2.CNRS, LIRMM, CNRS UMR55076, Université Montpellier 2MontpellierFrance
  3. 3.Department of MathematicsSimon Fraser UniversityBurnabyCanada
  4. 4.INRIA, LBBE, CNRS UMR5558, Université de Lyon 1VilleurbanneFrance

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