Easy Identification of Generalized Common and Conserved Nested Intervals

نویسندگان

  • Fabien de Montgolfier
  • Mathieu Raffinot
  • Irena Rusu
چکیده

In this article we explain how to easily compute gene clusters, formalized by classical or generalized nested common or conserved intervals, between a set of K genomes represented as K permutations. A b-nested common (resp. conserved) interval I of size |I| is either an interval of size 1 or a common (resp. conserved) interval that contains another b-nested common (resp. conserved) interval of size at least |I|-b. When b=1, this corresponds to the classical notion of nested interval. We exhibit two simple algorithms to output all b-nested common or conserved intervals between K permutations in O(Kn+nocc) time, where nocc is the total number of such intervals. We also explain how to count all b-nested intervals in O(Kn) time. New properties of the family of conserved intervals are proposed to do so.

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عنوان ژورنال:
  • Journal of computational biology : a journal of computational molecular cell biology

دوره 21 7  شماره 

صفحات  -

تاریخ انتشار 2014