Synthetic sequence design for signal location search

  • Authors:

  • Yaw-Ling Lin;Charles Ward;Steven Skiena

  • Affiliations:

  • Department of Computer Science and Information Engineering, Providence University, Taichung, Taiwan;Department of Computer Science, Stony Brook University, Stony Brook, NY;Department of Computer Science, Stony Brook University, Stony Brook, NY

  • Venue:
  • RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
  • Year:
  • 2012

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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.