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Working on the Problem of Sorting by Transpositions on Genome Rearrangements

  • Maria Emilia M. T. Walter
  • Luiz Reginaldo A. F. Curado
  • Adilton G. Oliveira
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2676)

Abstract

In computational biology, genome rearrangements is a field in which we investigate the combinatorial problem of sorting by transpositions. This problem consists in finding the minimum number of transpositions (mutational event) that transform a chromosome into another. In this work, we implement the 1.5-approximation algorithm proposed by Christie [2] for solving this problem, introducing modifications to reduce its time complexity, and we also propose heuristics to further improve its performance. Comparing our experimental results with the best known results, we had better performance. This work targets to contribute for discovering the complexity of the problem of sorting by transpositions, which remains open.

Keywords

Time Complexity Genome Rearrangement Oriented Cycle Cycle Graph Black Edge 
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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References

  1. 1.
    V. Bafna and P. Pevzner. Sorting by transpositions. In Proceedings of the 6th Annual ACM-SIAM Symposium on Discrete Algorithms, pages 614–623, 1995.Google Scholar
  2. 2.
    D. A. Christie. Genome rearrangements problems. PhD thesis, Glasgow University, Scotland, 1998.Google Scholar
  3. 3.
    Z. Dias and J. Meidanis. Sorting by prefix transpositions. In String Processing and Information Retrieval — SPIRE 2002, 2002. Lecture Notes in Computer Science, v. 2476, 2002.CrossRefGoogle Scholar
  4. 4.
    S. A. Guyer, L. S. Heath, and J. P. C. Vergara. Subsequences and run heuristics for sorting by transpositions. In 4th Dimacs International Algorithm Implementation Challenge, 1995.Google Scholar
  5. 5.
    J. Meidanis, M. E. M. T. Walter, and Z. Dias. Transposition distance of strictly decreasing sequences. In Workshop on String Processing-WSP 97, 1997.Google Scholar
  6. 6.
    E. T. G. Oliveira. Implementations of algorithms to the problem of sorting by transpositions. Master’s thesis, Department of Computer Science, University of Brasilia, 2001.Google Scholar
  7. 7.
    J. P. C. Vergara. Sorting by Bounded Permutations. PhD thesis, Virginia Polytechnic Institute and State University, 1997.Google Scholar
  8. 8.
    M. E. M. T. Walter, Z. Dias, and J. Meidanis. A new approach for approximating the transposition distance. In String Processing and Information Retrieval-SPIRE 2000, pages 199–208, 2000.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Maria Emilia M. T. Walter
    • 1
  • Luiz Reginaldo A. F. Curado
    • 1
  • Adilton G. Oliveira
    • 1
  1. 1.Department of Computer ScienceUniversity of BrasiliaBrasiliaBrasil

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