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Approximation and Nonapproximability for the One-Sided Scaffold Filling Problem

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Computing and Combinatorics (COCOON 2015)

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Abstract

Scaffold filling is an interesting combinatorial optimization problem from genome sequencing. The one-sided scaffold filling problem can be stated as: given an incomplete scaffold with some genes missing and a reference scaffold, the purpose is to insert the missing genes back into the incomplete scaffold( called ”filling the scaffold”), such that the number of common adjacencies between the filled scaffold and the reference scaffold is maximized. This problem is NP-hard for genome with duplicated genes, and can be approximated within 1.25 by a very complicated combinatorial method. In this paper, we firstly improve the approximation factor to 6/5 by not-oblivious local search; then we show that this problem is MAX-SNP-complete.

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Author information

Authors and Affiliations

  1. School of Computer Science and Technology, Shandong University, Jinan, 250101, People’s Republic of China

    Haitao Jiang, Jingjing Ma, Junfeng Luan & Daming Zhu

Authors
  1. Haitao Jiang
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  2. Jingjing Ma
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  3. Junfeng Luan
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  4. Daming Zhu
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Corresponding author

Correspondence to Haitao Jiang .

Editor information

Editors and Affiliations

  1. Beijing University of Technology, Beijing, China

    Dachuan Xu

  2. University of New Brunswick, Fredericton, Canada

    Donglei Du

  3. University of Texas at Dallas, Richardson, USA

    Dingzhu Du

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Jiang, H., Ma, J., Luan, J., Zhu, D. (2015). Approximation and Nonapproximability for the One-Sided Scaffold Filling Problem. In: Xu, D., Du, D., Du, D. (eds) Computing and Combinatorics. COCOON 2015. Lecture Notes in Computer Science(), vol 9198. Springer, Cham. https://doi.org/10.1007/978-3-319-21398-9_20

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  • DOI: https://doi.org/10.1007/978-3-319-21398-9_20

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-21397-2

  • Online ISBN: 978-3-319-21398-9

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