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Bounds for Resequencing by Hybridization

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Algorithms in Bioinformatics (WABI 2003)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 2812))

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Abstract

We study the problem of finding the sequence of an unknown DNA fragment given the set of its k-long subsequences and a homologous sequence, namely a sequence that is similar to the target sequence. Such a sequence is available in some applications, e.g., when detecting single nucleotide polymorphisms. Pe’er and Shamir studied this problem and presented a heuristic algorithm for it. In this paper, we give an algorithm with provable performance: We show that under some assumptions, the algorithm can reconstruct a random sequence of length O(4k) with high probability. We also show that no algorithm can reconstruct sequences of length Ω(logk·4k).

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Author information

Authors and Affiliations

  1. Dept. of Computer Science, Tel Aviv University,  

    Dekel Tsur

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  1. Dekel Tsur
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Editor information

Editors and Affiliations

  1. Department of Biomathematical Sciences, The Mount Sinai School of Medicine, 10029-6574, New York, NY

    Gary Benson

  2. Institute of Biomedical and Life Sciences, Division of Environmental and Evolutionary Biology, University of Glasgow, G12 8QQ, Glasgow, Scotland

    Roderic D. M. Page

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© 2003 Springer-Verlag Berlin Heidelberg

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Tsur, D. (2003). Bounds for Resequencing by Hybridization. In: Benson, G., Page, R.D.M. (eds) Algorithms in Bioinformatics. WABI 2003. Lecture Notes in Computer Science(), vol 2812. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-39763-2_35

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  • DOI: https://doi.org/10.1007/978-3-540-39763-2_35

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-20076-5

  • Online ISBN: 978-3-540-39763-2

  • eBook Packages: Springer Book Archive

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