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Fast sorting by reversal

  • Piotr Berman
  • Sridhar Hannenhalli
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1075)

Abstract

Analysis of genomes evolving by inversions leads to a combinatorial problem of sorting by reversals studied in detail recently. Following a series of work recently, Hannenhalli and Pevzner developed the first polynomial algorithm for the problem of sorting signed permutations by reversals and proposed an O(n4) implementation of the algorithm. In this paper we exploit a few combinatorial properties of the cycle graph of a permutation and propose an O(n2α(n)) implementation of the algorithm where α is the inverse Ackerman function. Besides making this algorithm practical, our technique improves implementations of the other rearrangement distance problems.

Keywords

Genome Rearrangement Polynomial Algorithm Unoriented Component Identity Permutation Oriented Cycle 
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 1996

Authors and Affiliations

  • Piotr Berman
    • 1
  • Sridhar Hannenhalli
    • 2
  1. 1.Department of Computer Science and EngineeringThe Pennsylvania State UniversityUniversity Park
  2. 2.Department of MathematicsUniversity of Southern CaliforniaLos Angeles

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