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Synthetic Sequence Design for Signal Location Search

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Research in Computational Molecular Biology (RECOMB 2012)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7262))

Abstract

We present a new approach to identify the locations of critical DNA or RNA sequence signals which couples large-scale synthesis with sophisticated designs employing combinatorial group testing and balanced Gray codes. Experiments in polio and adenovirus demonstrate the efficiency and generality of this procedure. In this paper, we give a new class of consecutive positive group testing designs, which offer a better tradeoff of cost, resolution, and robustness than previous designs for signal search.

Let n denote the number of distinct regions in a sequence, and d the maximum number of consecutive positives regions which can occur. We propose a design which improves on the consecutive-positive group testing designs of Colbourn. Our design completely identifies the boundaries of the positive region using t tests, where t ≈ log2(1.27n/d) + 0.5 log2(log2 (1.5 n /d) ) + d.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Information Engineering, Providence University, 200 Chung Chi Road, Shalu, Taichung, Taiwan, 433

    Yaw-Ling Lin

  2. Department of Computer Science, Stony Brook University, Stony Brook, NY, 11794-4400, USA

    Charles Ward & Steven Skiena

Authors
  1. Yaw-Ling Lin
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  2. Charles Ward
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  3. Steven Skiena
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Editor information

Editors and Affiliations

  1. Computer Science Department, Tel-Aviv University, 69978, Tel-Aviv, Israel

    Benny Chor

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© 2012 Springer-Verlag Berlin Heidelberg

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Lin, YL., Ward, C., Skiena, S. (2012). Synthetic Sequence Design for Signal Location Search. In: Chor, B. (eds) Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science(), vol 7262. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29627-7_15

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  • DOI: https://doi.org/10.1007/978-3-642-29627-7_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-29626-0

  • Online ISBN: 978-3-642-29627-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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