CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2009 vol.6 Issue No.04  OctoberDecember
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Issue No.04  OctoberDecember (2009 vol.6)
pp: 652666
Hiroaki Uehara , Keio University, Yokohama
Masakazu Jimbo , Nagoya University, Nagoya
ABSTRACT
The study of gene functions requires highquality DNA libraries. However, a large number of tests and screenings are necessary for compiling such libraries. We describe an algorithm for extracting as much information as possible from pooling experiments for library screening. Collections of clones are called pools, and a pooling experiment is a group test for detecting all positive clones. The probability of positiveness for each clone is estimated according to the outcomes of the pooling experiments. Clones with high chance of positiveness are subjected to confirmatory testing. In this paper, we introduce a new positive clone detecting algorithm, called the Bayesian network pool result decoder (BNPD). The performance of BNPD is compared, by simulation, with that of the Markov chain pool result decoder (MCPD) proposed by Knill et al. in 1996. Moreover, the combinatorial properties of pooling designs suitable for the proposed algorithm are discussed in conjunction with combinatorial designs and d\hbox{}{\rm disjunct} matrices. We also show the advantage of utilizing packing designs or BIB designs for the BNPD algorithm.
INDEX TERMS
DNA library screening, highthroughput screening, pooling experiment, two stage test, group testing, Bayesian network, sumproduct algorithm, LDPC.
CITATION
Hiroaki Uehara, Masakazu Jimbo, "A Positive Detecting Code and Its Decoding Algorithm for DNA Library Screening", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.6, no. 4, pp. 652666, OctoberDecember 2009, doi:10.1109/TCBB.2007.70266
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