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A Lin-Kernighan Heuristic for the DCJ Median Problem of Genomes with Unequal Contents

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Computing and Combinatorics (COCOON 2014)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8591))

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Abstract

In this paper, we designed a distance metric as DCJ-Indel-Exemplar distance to estimate the dissimilarity between two genomes with unequal contents (with gene insertions/deletions (Indels) and duplications). Based on the aforementioned distance metric, we proposed the DCJ-Indel-Exemplar median problem, to find a median genome that minimize the DCJ-Indel-Exemplar distance between this genome and the given three genomes. We adapted Lin-Kernighan (LK) heuristic to calculate the median quickly by utilizing the features of adequate sub-graph decomposition and search space reduction technologies. Experimental results on simulated gene order data indicate that our distance estimator can closely estimate the real number of rearrangement events; while compared with the exact solver using equal content genomes, our median solver can get very accurate results as well. More importantly, our median solver can deal with Indels and duplications and generates results very close to the synthetic cumulative number of evolutionary events.

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Author information

Authors and Affiliations

  1. School of Computer Science and Technology, Tianjin University, China

    Jijun Tang

  2. School of Compuational Science and Engineering, Georgia Institute of Technology, USA

    Zhaoming Yin & David A. Bader

  3. Dept. of Computer Science and Engineering, University of South Carolina, USA

    Jijun Tang

  4. The Huck Institutes of Life Sciences, Pennsylvania State University, USA

    Stephen W. Schaeffer

Authors
  1. Zhaoming Yin
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  2. Jijun Tang
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  3. Stephen W. Schaeffer
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  4. David A. Bader
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Editors and Affiliations

  1. Department of Computer Science, Georgia State University, 34 Peachtree Street, Suite 1410, 30303, Atlanta, GA, USA

    Zhipeng Cai

  2. Department of Computer Science, Georgia State University, 34 Peachtree Street, Suite 1443, 30303, Atlanta, GA, USA

    Alex Zelikovsky

  3. Department of Computer Science, Georgia State University, 34 Peachtree Street, Suite 1449, 30303, Atlanta, GA, USA

    Anu Bourgeois

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Yin, Z., Tang, J., Schaeffer, S.W., Bader, D.A. (2014). A Lin-Kernighan Heuristic for the DCJ Median Problem of Genomes with Unequal Contents. In: Cai, Z., Zelikovsky, A., Bourgeois, A. (eds) Computing and Combinatorics. COCOON 2014. Lecture Notes in Computer Science, vol 8591. Springer, Cham. https://doi.org/10.1007/978-3-319-08783-2_20

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  • DOI: https://doi.org/10.1007/978-3-319-08783-2_20

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-08782-5

  • Online ISBN: 978-3-319-08783-2

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