A Linear Kernel for the Complementary Maximal Strip Recovery Problem

  • Haitao Jiang
  • Binhai Zhu
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7354)

Abstract

In this paper, we compute the first linear kernel for the complementary problem of Maximal Strip Recovery (CMSR) — a well-known NP-complete problem in computational genomics. Let k be the parameter which represents the size of the solution. The core of the technique is to first obtain a tight 18k bound on the parameterized solution search space, which is done through a mixed global rules and local rules, and via an inverse amortized analysis. Then we apply additional data-reduction rules to obtain a tight 84k kernel for the problem. Combined with the known algorithm using bounded degree search, we obtain the best FPT algorithm for CMSR to this date, running in O(2.36kk2 + n2) time.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Haitao Jiang
    • 1
    • 2
  • Binhai Zhu
    • 3
  1. 1.School of Computer Science and TechnologyShandong UniversityJinanChina
  2. 2.School of Mathematics and System ScienceShandong UniversityJinanChina
  3. 3.Department of Computer ScienceMontana State UniversityBozemanUSA

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