Algorithmica

, Volume 28, Issue 3, pp 323–352

Sorting by Short Block-Moves

  • L. S. Heath
  • J. P. C. Vergara
Article

Abstract.

Sorting permutations by operations such as reversals and block-moves has received much interest because of its applications in the study of genome rearrangements and in the design of interconnection networks. A short block-move is an operation on a permutation that moves an element at most two positions away from its original position. This paper investigates the problem of finding a minimum-length sorting sequence of short block-moves for a given permutation. A 4/3 -approximation algorithm for this problem is presented. Woven double-strip permutations are defined and a polynomial-time algorithm for this class of permutations is devised that employs graph matching techniques. A linear-time maximum matching algorithm for a special class of grid graphs improves the time complexity of the algorithm for woven double-strip permutations.

Key words. Computational biology, Genome rearrangement, Approximation algorithms, Maximum matching, Permutations. 

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Copyright information

© Springer-Verlag 2000

Authors and Affiliations

  • L. S. Heath
    • 1
  • J. P. C. Vergara
    • 2
  1. 1.Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0106, USA. heath@cs.vt.edu.US
  2. 2.Department of Information Systems and Computer Science, Ateneo De Manila University, Manila 0917, Philippines. jpv@admu.edu.ph.PH

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