Abstract
Tandem repeated regions are closely related to some genetic diseases in human beings. Once a region containing pseudo-periodic repeats is found, it is interesting to study the history of creating the repeats. It is important to reveal the relationship between repeats and genetic diseases. The duplication model has been proposed to describe the history [3,10,11]. We design a polynomial time approximation scheme (PTAS) for the case where the size of the duplication box is 1. Our PTAS is faster than the best known algorithm in [11]. For example, to reach ratio-1.5, our algorithm takes O(n 5) time while the algorithm in [11] takes O(n 11) time. We also design a ratio-2 approximation algorithm for the case where the size of the duplication box is at most 2. This is the first approximation algorithm with guaranteed ratio for this case.
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Boby, T., Patch, A.-M., Aves, S.J.: TRbase: a database relating tandem repeats to disease genes for the human genome. Bioinformatics, Advance Access published on (October 12, 2004)
Subramanian, S., Mishra, R.K., Singh, L.: Genome-wide analysis of Bkm sequences (GATA repeats): predominant association with sex chromosomes and potential role in higher order chromatin organization and function. Bioinformatics 19, 681–685 (2003)
Fitch, W.: Phylogenies constrained by cross-over process as illustrated by human hemoglobins in a thirteen cycle, eleven amino-acid repeat in human apolipoprotein A-I. Genetics 86, 623C644 (1977)
Zhang, L., Ma, B., Wang, L., Xu, Y.: Greedy method for inferring tandem duplication history. Bioinformatics 19, 1497–1504 (2003)
Otu, H.H., Sayood, K.: A new sequence distance measure for phylogenetic tree construction. Bioinformatics 19, 2122–2130 (2003)
Macas, J., Mszros, T., Nouzov, M.: PlantSat: a specialized database for plant satellite repeats. Bioinformatics 18, 28–35 (2002)
Lillo, F., Basile, S., Mantegna, R.N.: Comparative genomics study of inverted repeats in bacteria. Bioinformatics 18, 971–979 (2002)
Benson, G., Dong, L.: Reconstructing the duplication history of a tandem repeat. In: Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB-99), pp. 44–53 (1999)
Widegren, B., Arnason, U., Akusjarvi, G.: Characteristics of a conserved 1,579-bp highly repetitive component in the killer whale, Ornicus orca. Mol. Biol. Evol. 2, 411–419 (1985)
Tang, M., Waterman, M.S., Yooseph, S.: Zinc Finger Gene Clusters and Tandem Gene Duplication. Journal of Computational Biology 9(2), 429–446 (2002)
Jaitly, D., Kearney, P.E., Lin, G.-H., Ma, B.: Methods for reconstructing the history of tandem repeats and their application to the human genome. J. Comput. Syst. Sci. 65(3), 494–507 (2002)
Wyman, A.H., White, R.: A highly polymorphic locus in human DNA. Proc. Natl. Acad. Sci. 77, 6745–6758 (1980)
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Wang, L., Wang, Z., Chen, Z. (2007). Approximation Algorithms for Reconstructing the Duplication History of Tandem Repeats. In: Lin, G. (eds) Computing and Combinatorics. COCOON 2007. Lecture Notes in Computer Science, vol 4598. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73545-8_48
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DOI: https://doi.org/10.1007/978-3-540-73545-8_48
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-73544-1
Online ISBN: 978-3-540-73545-8
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