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Perfect Sorting by Reversals Is Not Always Difficult

  • Sèverine Bérard
  • Anne Bergeron
  • Cedric Chauve
  • Christophe Paul
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3692)

Abstract

This paper investigates the problem of conservation of combinatorial structures in genome rearrangement scenarios. We characterize a class of signed permutations for which one can compute in polynomial time a reversal scenario that conserves all common intervals, and that is parsimonious among such scenarios. Figeac and Varré (WABI 2004) announced that the general problem is NP-hard. We show that there exists a class of permutations for which this computation can be done in linear time with a very simple algorithm, and, for a larger class of signed permutations, the computation can be achieved in subquadratic time. We apply these methods to permutations obtained from the X chromosomes of the human, mouse and rat.

Keywords

Prime Node Permutation Graph Identity Permutation Common Interval Reversal Scenario 
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

  • Sèverine Bérard
    • 1
  • Anne Bergeron
    • 2
  • Cedric Chauve
    • 2
  • Christophe Paul
    • 3
  1. 1.Dépt. de Mathématique et Informatique AppliquéeINRA ToulouseFrance
  2. 2.LaCIM et Dépt. d’InformatiqueUniversité du Québec à MontréalCanada
  3. 3.CNRS, LIRMMMontpellierFrance

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