Journal of Microbiology and Biotechnology
The Korean Society for Microbiology and Biotechnology publishes the Journal of Microbiology and Biotechnology.
Journal of Microbiology and Biotechnology
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2006 ; 16(5): 683~688

AuthorHur Cheol-Goo, Sunny Kim, Chang Hoon Kim, Sung Ho Yoon, Yong-Ho In, Cheolmin Kim, Hwan Gue Cho
AffiliationDivision of Genomics and Proteomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejon 305-333, Korea
TitleFASIM: Fragments Assembly Simulation using Biased-Sampling Model and Assembly Simulation for Microbial Genome Shotgun Sequencing
PublicationInfo J. Microbiol. Biotechnol.2006 16(5): 683~688
AbstractWe have developed a program for generating shotgun data sets from known genome sequences. Generation of synthetic data sets by computer program is a useful alternative to real data to which students and researchers have limited access. Uniformly-distributed-sampling clones that were adopted by previous programs cannot account for the real situation where sampled reads tend to come from particular regions of the target genome. To reflect such situation, a probabilistic model for biased sampling distribution was developed by using an experimental data set derived from a microbial genome project. Among the experimental parameters tested (varied fragment or read lengths, chimerism, and sequencing error), the extent of sequencing error was the most critical factor that hampered sequence assembly. We propose that an optimum sequencing strategy employing different insert lengths and redundancy can be established by performing a variety of simulations.
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KeywordsFragments assembly simulation, sampling model, genome, shotgun sequencing



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