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Optimal Probing Patterns for Sequencing by Hybridization

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Algorithms in Bioinformatics (WABI 2006)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4175))

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Abstract

Sequencing by Hybridization (SBH) is a method for reconstructing a DNA sequence based on its k-mer content. This content, called the spectrum of the sequence, can be obtained from hybridization with a universal DNA chip. The main shortcoming of SBH is that it reliably reconstructs only sequences of length at most square root of the size of the chip. Frieze et al. [9] showed that by using gapped probes, SBH can reconstruct sequences with length that is linear in the size of the chip. In this work we investigate the optimal placement of the gaps in the probes, and give an algorithm for finding nearly optimal gap placement. Using our algorithm, we obtain a chip design which is more efficient than the chip of Frieze et al.

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Author information

Authors and Affiliations

  1. Department of Computer Science, Ben-Gurion University of the Negev,  

    Dekel Tsur

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  1. Dekel Tsur
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Editor information

Editors and Affiliations

  1. Ecole Polytechnique Fédérale de Lausanne, Switzerland

    Philipp Bücher

  2. Laboratory for Computational Biology and Bioinformatics, EPFL (Ecole Polytechnique Fédérale de Lausanne), Swiss Institute of Bioinformatics, Lausanne, Switzerland

    Bernard M. E. Moret

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© 2006 Springer-Verlag Berlin Heidelberg

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Tsur, D. (2006). Optimal Probing Patterns for Sequencing by Hybridization. In: Bücher, P., Moret, B.M.E. (eds) Algorithms in Bioinformatics. WABI 2006. Lecture Notes in Computer Science(), vol 4175. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11851561_34

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  • DOI: https://doi.org/10.1007/11851561_34

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-39583-6

  • Online ISBN: 978-3-540-39584-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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