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Journal of Combinatorial Optimization

, Volume 23, Issue 4, pp 519–527 | Cite as

Minimum common string partition revisited

  • Haitao Jiang
  • Binhai Zhu
  • Daming Zhu
  • Hong Zhu
Article

Abstract

Minimum Common String Partition (MCSP) has drawn much attention due to its application in genome rearrangement. In this paper, we investigate three variants of MCSP: MCSP c , which requires that there are at most c elements in the alphabet; d-MCSP, which requires the occurrence of each element to be bounded by d; and x-balanced MCSP, which requires the length of blocks being in range (n/kx,n/k+x), where n is the length of the input strings, k is the number of blocks in the optimal common partition and x is a constant integer. We show that MCSP c is NP-hard when c≥2. As for d-MCSP, we present an FPT algorithm which runs in O ((d!)2k ) time. As it is still unknown whether an FPT algorithm only parameterized on k exists for the general case of MCSP, we also devise an FPT algorithm for the special case x-balanced MCSP parameterized on both k and x.

Keywords

Minimum common string partition Genomic distance Genome rearrangement NP-completeness FPT algorithms 

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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Haitao Jiang
    • 1
    • 2
  • Binhai Zhu
    • 1
  • Daming Zhu
    • 2
  • Hong Zhu
    • 3
  1. 1.Department of Computer ScienceMontana State UniversityBozemanUSA
  2. 2.School of Computer Science and TechnologyShandong UniversityJinanChina
  3. 3.College of SoftwareEast China Normal UniversityShanghaiChina

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