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Synthetic Sequence Design for Signal Location Search

  • Yaw-Ling Lin
  • Charles Ward
  • Steven Skiena
Part of the Lecture Notes in Computer Science book series (LNCS, 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.

Keywords

Combinatorial group testing non-adaptive group testing Gray codes synthetic biology 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Yaw-Ling Lin
    • 1
  • Charles Ward
    • 2
  • Steven Skiena
    • 2
  1. 1.Department of Computer Science and Information EngineeringProvidence UniversityTaichungTaiwan
  2. 2.Department of Computer ScienceStony Brook UniversityStony BrookUSA

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