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Synthetic Sequence Design for Signal Location Search

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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)+0.5log2(log2(1.5n/d))+d.

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Acknowledgements

We would like to thank our experimental collaborators in Wadie Bahou and Eckard Wimmer’s groups, and Ian Shields for providing the middle level Hamiltonian cycles which were used to create our group testing designs. This work was partially supported by NIH Grant AI075219 and NSF Grants DBI-1060572 and IIS-1017181.

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Authors and Affiliations

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

    Yaw-Ling Lin

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

    Charles Ward & Steven Skiena

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  1. Yaw-Ling Lin
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  2. Charles Ward
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Correspondence to Charles Ward.

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Lin, YL., Ward, C. & Skiena, S. Synthetic Sequence Design for Signal Location Search. Algorithmica 67, 368–383 (2013). https://doi.org/10.1007/s00453-013-9760-9

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