Advertisement

Solving the Minimum Common String Partition Problem with the Help of Ants

  • S. M. Ferdous
  • M. Sohel Rahman
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7928)

Abstract

In this paper, we consider the problem of finding minimum common partition of two strings (MCSP). The problem has its application in genome comparison. As it is an NP-hard, discrete combinatorial optimization problem, we employ a metaheuristic technique, namely, MAX-MIN ant system to solve this. The preliminary experimental results are found to be promising.

Keywords

Ant Colony Optimization Stringology Genome sequencing Combinatorial Optimization Swarm Intelligence String partition 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Dorigo, M., Di Caro, G., Gambardella, M.L.: Ant algorithms for discrete optimization. J. of Artificial Life 5(2), 137–172 (1999)CrossRefGoogle Scholar
  2. 2.
    Dorigo, M., Gambardella, M.L.: Ant Colony System: A Cooperative Learning Approach to the Traveling Salesman Problem. J. of IEEE Transactions on Evolutionary Computation 1 (1996)Google Scholar
  3. 3.
    Stuetzle, T., Hoos, H.H.: MAX-MIN Ant System. J. of Future Gener. Comput. System 16(9), 889–914 (2000)CrossRefGoogle Scholar
  4. 4.
    Watterson, G.A., Ewens, W.J., Hall, T.E., Morgan, A.: The chromosome inversion problem. Journal of Theoretical Biology 99, 7 (1982)CrossRefGoogle Scholar
  5. 5.
    Goldstein, A., Kolman, P., Zheng, J.: Minimum common string partition problem: Hardness and approximations. In: Fleischer, R., Trippen, G. (eds.) ISAAC 2004. LNCS, vol. 3341, pp. 484–495. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  6. 6.
    Chen, X., Zheng, J., Fu, Z., Nan, P., Zhong, Y., Lonardi, S., Jiang, T.: Assignment of orthologous genes via genome rearrangement (2004) (submitted)Google Scholar
  7. 7.
    Damaschke, P.: Minimum Common String Partition Parameterized. In: Crandall, K.A., Lagergren, J. (eds.) WABI 2008. LNCS (LNBI), vol. 5251, pp. 87–98. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  8. 8.
    Chrobak, M., Kolman, P., Sgall, J.: The greedy algorithm for the minimum common string partition problem. In: Jansen, K., Khanna, S., Rolim, J.D.P., Ron, D. (eds.) APPROX and RANDOM 2004. LNCS, vol. 3122, pp. 84–95. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  9. 9.
    Jiang, H., Zhu, B., Zhu, D., Zhu, H.: Minimum common string partition revisited. In: Lee, D.-T., Chen, D.Z., Ying, S. (eds.) FAW 2010. LNCS, vol. 6213, pp. 45–52. Springer, Heidelberg (2010)CrossRefGoogle Scholar
  10. 10.
    Stothard, P.: The Sequence Manipulation Suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 28, 1102–1104 (2000)Google Scholar
  11. 11.
    Villesen, P.: FaBox: an online fasta sequence toolbox (2007), http://www.birc.au.dk/software/fabox

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • S. M. Ferdous
    • 1
  • M. Sohel Rahman
    • 1
  1. 1.AℓEDA Group, Department of CSEBUETDhakaBangladesh

Personalised recommendations