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Sorting by Reversals with Common Intervals

  • Martin Figeac
  • Jean-Stéphane Varré
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3240)

Abstract

Studying rearrangements from gene order data is a standard approach in evolutionary analysis. Gene order data are usually modeled as signed permutations. The computation of the minimal number of reversals between two signed permutations produced a lot of literature during the last decade. Algorithms designed were first approximative, then polynomial and were further improved to give a linear one. Several extensions were investigated authorizing for example deletion or insertion of genes during the sorting process. We propose to revisit the ’sorting by reversals’ problem by adding constraints on allowed reversals. We do not allow to break conserved clusters of genes usually called Common Intervals. We show that this problem is NP-complete. Assuming special conditions, we propose a polynomial algorithm.

Omitted proofs are given as supplementary material at http://www.lifl.fr/~figeac/supplementary_material/srac_appendix.pdf

Keywords

Polynomial Algorithm Exponential Time Sorting Process Consecutive Block Identity Permutation 
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 2004

Authors and Affiliations

  • Martin Figeac
    • 1
  • Jean-Stéphane Varré
    • 1
  1. 1.Laboratoire d’Informatique Fondamentale de LilleUniversité des sciences et technologies de LilleVilleneuve d’Ascq CedexFrance

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