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    National Tsing Hua University Institutional Repository > 電機資訊學院 > 資訊工程學系 > 期刊論文 >  Constrained sequence alignment: a general model and the hardness results

    Please use this identifier to cite or link to this item: http://nthur.lib.nthu.edu.tw/dspace/handle/987654321/66327

    Title: Constrained sequence alignment: a general model and the hardness results
    Authors: Yun-Sheng Chung;Chin Lung Lu;Chuan Yi Tang
    教師: 唐傳義
    Date: 2007
    Publisher: Elsevier
    Relation: Discrete Applied Mathematics,Volume 155,Issue 18,1 November 2007,Pages 2471-2486
    Keywords: sequence alignment
    constrained alignment
    Abstract: Imposing constraints is a way to incorporate information into the sequence alignment procedure. In this paper, a general model for constrained alignment is proposed so that analyses admitted are more flexible and that different pattern definitions can be treated in a simple unified way. We give a polynomial time algorithm for pairwise constrained alignment for the generalized formulation, and prove the inapproximability of the problem when the number of sequences can be arbitrary. In addition, previous works deal only with the case that the patterns in the constraint have to occur in the output alignment in the same order as that specified by the input. It is of both theoretical and practical interest to investigate the case when the order is no longer limited. We show that the problem is not approximable even when the number of sequences is two. We also give the NPO-completeness results for the problems with bounds imposed on the objective function value.
    URI: http://www.elsevier.com/
    Appears in Collections:[資訊工程學系] 期刊論文

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