DocumentCode :
981053
Title :
A Positive Detecting Code and Its Decoding Algorithm for DNA Library Screening
Author :
Uehara, Hiroaki ; Jimbo, Masakazu
Author_Institution :
Dept. of Math., Keio Univ., Yokohama, Japan
Volume :
6
Issue :
4
fYear :
2009
Firstpage :
652
Lastpage :
666
Abstract :
The study of gene functions requires high-quality 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-disjunct matrices. We also show the advantage of utilizing packing designs or BIB designs for the BNPD algorithm.
Keywords :
DNA; Markov processes; belief networks; decoding; genetics; molecular biophysics; Bayesian network; DNA library screening; Markov chain pool; combinatorial property; confirmatory testing; d-disjunct matrices; decoding algorithm; gene functions; pooling experiment; positive clone detecting algorithm; positive detecting code; Algorithms; Bayesian network; Biology and genetics; DNA library screening; LDPC.; group testing; high-throughput screening; pooling experiment; sum-product algorithm; two stage test; Algorithms; Bayes Theorem; Chromosome Mapping; Chromosomes; Computational Biology; Gene Library; Genome, Human; Humans; Markov Chains; Pattern Recognition, Automated; Sequence Analysis, DNA; Software;
fLanguage :
English
Journal_Title :
Computational Biology and Bioinformatics, IEEE/ACM Transactions on
Publisher :
ieee
ISSN :
1545-5963
Type :
jour
DOI :
10.1109/TCBB.2007.70266
Filename :
4384569
Link To Document :
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