Sorting circular permutations by bounded transpositions

Adv Exp Med Biol. 2010:680:725-36. doi: 10.1007/978-1-4419-5913-3_81.

Abstract

A k-bounded (k ≥ 2) transposition is an operation that switches two elements that have at most k - 2 elements in between. We study the problem of sorting a circular permutation π of length n for k = 2, i.e., adjacent swaps and k = 3, i.e., short swaps. These transpositions mimic microrearrangements of gene order in viruses and bacteria. We prove a (1/4)n (2) lower bound for sorting by adjacent swaps. We show upper bounds of (5/32)n (2) + O(n log n) and (7/8)n + O(log n) for sequential and parallel sorting, respectively, by short swaps.

MeSH terms

  • Algorithms
  • Animals
  • Computational Biology
  • Computer Simulation
  • Evolution, Molecular
  • Gene Order
  • Gene Rearrangement*
  • Humans
  • Models, Genetic*