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Linear-Time Algorithms for the Multiple Gene Duplication Problems
January-February 2011 (vol. 8 no. 1)
pp. 260-265
Cheng-Wei Luo, National Taiwan University, Taipei
Ming-Chiang Chen, National Taiwan University, Taipei
Yi-Ching Chen, National Taiwan University, Taipei
Roger W.L. Yang, National Taiwan University, Taipei
Hsiao-Fei Liu, National Taiwan University, Taipei
Kun-Mao Chao, National Taiwan University, Taipei
A fundamental problem arising in the evolutionary molecular biology is to discover the locations of gene duplications and multiple gene duplication episodes based on the phylogenetic information. The solutions to the MULTIPLE GENE DUPLICATION problems can provide useful clues to place the gene duplication events onto the locations of a species tree and to expose the multiple gene duplication episodes. In this paper, we study two variations of the MULTIPLE GENE DUPLICATION problems: the EPISODE-CLUSTERING (EC) problem and the MINIMUM EPISODES (ME) problem. For the EC problem, we improve the results of Burleigh et al. with an optimal linear-time algorithm. For the ME problem, on the basis of the algorithm presented by Bansal and Eulenstein, we propose an optimal linear-time algorithm.

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Index Terms:
Computational phylogenetics, gene duplication, computations on discrete structures, linear-time algorithm.
Citation:
Cheng-Wei Luo, Ming-Chiang Chen, Yi-Ching Chen, Roger W.L. Yang, Hsiao-Fei Liu, Kun-Mao Chao, "Linear-Time Algorithms for the Multiple Gene Duplication Problems," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 1, pp. 260-265, Jan.-Feb. 2011, doi:10.1109/TCBB.2009.52
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