• Journal of Microbiology and Biotechnology
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• 제16권5호
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• pp.683-688
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• 2006

We 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.

• Genomics & Informatics
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• 제2권4호
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• pp.184-190
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• 2004

An approach for genome analysis based on assembly of fragments of DNA from the whole genome can be applied to obtain the complete nucleotide sequence of the genome of Zymomonas mobilis. However, the problem of fragment assembly raise thorny computational issues. Computer simulation studies of sequence assembly usually show some abnormal assemblage of artificial sequences containing repetitive or duplicated regions, and suggest methods to correct those abnormalities. In this paper, we describe five simulation studies which had been performed previous to the actual genome assembly process of Zymomonas mobilis ZM4.

• 대한기계학회논문집A
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• 제30권7호
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• pp.841-848
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• 2006

Many researchers are developing computational prediction methods for protein tertiary structures to get much more information of protein. These methods are very attractive on the aspects of breaking technologies of computer hardware and simulation software. One of the computational methods for the prediction is a fragment assembly method which shows good ab initio predictions at several cases. There are many barriers, however, in conventional fragment assembly methods. Argues on protein energy functions and global optimization to predict the structures are in progress fer example. In this study, a new prediction method for protein structures is proposed. The proposed method mainly consists of two parts. The first one is a fragment assembly which uses very shot fragments of representative proteins and produces a prototype of a given sequence query of amino acids. The second one is a global optimization which folds the prototype and makes the only protein structure. The goodness of the proposed method is shown through numerical experiments.