title: Hurdles and sorting by inversions: combinatorial, statistical, and experimental results.
abstract: 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 provide the first asymptotically tight analysis of the probability that a fortress exists in a random permutation. Finally, we study other aspects of hurdles, both analytically and through experiments: when are they created in a sequence of sorting inversions, how much later are they detected, and how much work may need to be undone to return to a sorting sequence.
authors.affiliation: Laboratory for Computational Biology and Bioinformatics, EPFL (Ecole Polytechnique Fédérale de Lausanne), and Swiss Institute of Bioinformatics, Lausanne, Switzerland. Krister.swenson@epfl.ch
authors.forename: Krister M
authors.initials: KM
authors.lastname: Swenson
authors.forename: Yu
authors.initials: Y
authors.lastname: Lin
authors.forename: Vaibhav
authors.initials: V
authors.lastname: Rajan
authors.forename: Bernard M E
authors.initials: BM
authors.lastname: Moret
mesh_terms: D000465:Algorithms; D015321:Gene Rearrangement; D016678:Genome; D023281:Genomics / Q000379:methods; D008433:Mathematics; D008957:Models, Genetic