Hurdles Hardly Have to Be Heeded

  • Krister M. Swenson
  • Yu Lin
  • Vaibhav Rajan
  • Bernard M. E. Moret
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5267)


As data about genomic architecture accumulates, genomic rearrangements have attracted increasing attention. One of the main rearrangement mechanisms, inversions (also called reversals), was characterized by Hannenhalli and Pevzner and this characterization in turn extended by various authors. The characterization relies on the concepts of breakpoints, cycles, and obstructions colorfully named hurdles and fortresses. In this paper, we study the probability of generating a hurdle in the process of sorting a permutation if one does not take special precautions to avoid them (as in a randomized algorithm, for instance). To do this we revisit and extend the work of Caprara and of Bergeron by providing simple and exact characterizations of the probability of encountering a hurdle in a random permutation. Using similar methods we, for the first time, find an asymptotically tight analysis of the probability that a fortress exists in a random permutation.


Random Permutation Genomic Architecture Frame Element Circular Permutation Common Interval 
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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© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Krister M. Swenson
    • 1
  • Yu Lin
    • 1
  • Vaibhav Rajan
    • 1
  • Bernard M. E. Moret
    • 1
  1. 1.Laboratory for Computational Biology and Bioinformatics, EPFL (Ecole Polytechnique Fédérale de Lausanne), and Swiss Institute of BioinformaticsLausanneSwitzerland

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