TY - GEN
T1 - Synthetic sequence design for signal location search
AU - Lin, Yaw Ling
AU - Ward, Charles
AU - Skiena, Steven
PY - 2012
Y1 - 2012
N2 - 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≈log 2(1.27n/d)+0.5 log 2(log 2 (1.5n/d) )+ d.
AB - 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≈log 2(1.27n/d)+0.5 log 2(log 2 (1.5n/d) )+ d.
KW - Combinatorial group testing
KW - Gray codes
KW - non-adaptive group testing
KW - synthetic biology
UR - https://www.scopus.com/pages/publications/84860826720
U2 - 10.1007/978-3-642-29627-7_15
DO - 10.1007/978-3-642-29627-7_15
M3 - Conference contribution
AN - SCOPUS:84860826720
SN - 9783642296260
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 165
EP - 179
BT - Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings
T2 - 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012
Y2 - 21 April 2012 through 24 April 2012
ER -