Decoding algorithms in pooling designs with inhibitors and error-tolerance

Authors:
My T. Thai;David MacCallum;Ping Deng;Weili Wu
Affiliations:
Department of Computer and Information Science and Engineering, University of Florida, P.O. Box 116120, Gainesville, FL 32611, USA.;Department of Computer Science, University of Minnesota, Twin Cities, 200 Union Street S.E., Minneapolis, MN 55455, USA.;Department of Computer Science, University of Texas at Dallas, Richardson, TX 75083, USA.;Department of Computer Science, University of Texas at Dallas, Richardson, TX 75083, USA
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2007

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Abstract

Pooling designs are used in DNA library screening to efficiently distinguish positive from negative clones, which is fundamental for studying gene functions and many other biological applications. One challenge is to design decoding algorithms for determining whether a clone is positive based on the test outcomes and a binary matrix representing the pools. This is more difficult in practice due to errors in biological experiments. More challenging still is a third category of clones called 'inhibitors' whose effect is to neutralise positives. We present a novel decoding algorithm identifying all positive clones in the presence of inhibitors and experimental errors.