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International Computing and Combinatorics Conference

COCOON 2018: Computing and Combinatorics pp 554–566Cite as

On a Fixed Haplotype Variant of the Minimum Error Correction Problem

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 10976))

Abstract

Haplotype assembly is the problem of reconstructing the two parental chromosomes of an individual from a set of sampled DNA-sequences. A combinatorial optimization problem that models haplotype assembly is the Minimum Error Correction problem (MEC). This problem has been intensively studied in the computational biology literature and is also known in the clustering literature: essentially we are required to find two cluster centres such that the sum of distances to the nearest centre, is minimized. We introduce here the problem Fixed haplotype-Minimum Error Correction (FH-MEC), a new variant of MEC which corresponds to instances where one of the haplotypes/centres is already given. We provide hardness results for the problem on various restricted instances. We also propose a new and very simple 2-approximation algorithm for MEC on binary input matrices.

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Notes

  1. 1.

    A binary matrix M is conflict-free if the rows of M can be bipartitioned into two sets such that the corresponding entries on each set are identical.

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Acknowledgements

The last author acknowledges the support of an NWO TOP 2 grant.

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Authors and Affiliations

  1. Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands

    Axel Goblet, Steven Kelk, Matúš Mihalák & Georgios Stamoulis

Authors
  1. Axel Goblet
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  2. Steven Kelk
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  3. Matúš Mihalák
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  4. Georgios Stamoulis
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Corresponding author

Correspondence to Georgios Stamoulis .

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Editors and Affiliations

  1. City University of Hong Kong, Hong Kong, China

    Lusheng Wang

  2. Shandong University, Jinan, China

    Daming Zhu

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Goblet, A., Kelk, S., Mihalák, M., Stamoulis, G. (2018). On a Fixed Haplotype Variant of the Minimum Error Correction Problem. In: Wang, L., Zhu, D. (eds) Computing and Combinatorics. COCOON 2018. Lecture Notes in Computer Science(), vol 10976. Springer, Cham. https://doi.org/10.1007/978-3-319-94776-1_46

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  • DOI: https://doi.org/10.1007/978-3-319-94776-1_46

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-94775-4

  • Online ISBN: 978-3-319-94776-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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