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Improved Algorithms for the Gene Team Problem

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Combinatorial Optimization and Applications (COCOA 2009)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5573))

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Abstract

A gene team is a set of genes that appear in two or more species, possibly in a different order yet with the distance between adjacent genes in the team for each chromosome always no more than a certain threshold. The focus of this paper is the problem of finding gene teams of two chromosomes. Béal et al. [1] had an O(nlog2 n)-time algorithm for this problem. In this paper, two O(nlogd)-time algorithms are proposed, where d ≤ n is the number of gene teams. The proposed algorithms are obtained by modifying Béal et al.’s algorithm, using two different approaches. Béal et al.’s algorithm can be extended to find the gene teams of k chromosomes in O(knlog2 n) time. Our improved algorithms can be extended to find the gene teams of k chromosomes in O(knlogd) time.

This research is supported by the National Science Council of the Republic of China under grant NSC-97-2221-E-007-053-MY3.

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Author information

Authors and Affiliations

  1. Department of Computer Science, National Tsing Hua University Hsinchu, 30043, Taiwan, Republic of China

    Biing-Feng Wang, Shang-Ju Liu & Chien-Hsin Lin

Authors
  1. Biing-Feng Wang
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  2. Shang-Ju Liu
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  3. Chien-Hsin Lin
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Editor information

Editors and Affiliations

  1. Department of Computer Science, University of Texas at Dallas, 800 West Campbell Road, TX 75080-3021, Richardson, USA

    Ding-Zhu Du

  2. Chinese Academy of Sciences, Institute of Applied Mathematics, Zhong Guan Cun Dong Lu 55, 100190, Beijing, P. R. China

    Xiaodong Hu

  3. Department of Industrial and Systems Engineering, University of Florida, 303 Weil Hall, P.O. Box 116595, FL 32611-6595, Gainesville, USA

    Panos M. Pardalos

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© 2009 Springer-Verlag Berlin Heidelberg

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Wang, BF., Liu, SJ., Lin, CH. (2009). Improved Algorithms for the Gene Team Problem. In: Du, DZ., Hu, X., Pardalos, P.M. (eds) Combinatorial Optimization and Applications. COCOA 2009. Lecture Notes in Computer Science, vol 5573. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02026-1_6

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  • DOI: https://doi.org/10.1007/978-3-642-02026-1_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-02025-4

  • Online ISBN: 978-3-642-02026-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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