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Bounds for Resequencing by Hybridization

  • Dekel Tsur
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2812)

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(4 k ) with high probability. We also show that no algorithm can reconstruct sequences of length Ω(logk·4 k ).

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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Dekel Tsur
    • 1
  1. 1.Dept. of Computer ScienceTel Aviv University 

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