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Genomics Inform > Volume 2(4); 2004 > Article
Five Computer Simulation Studies of Whole-Genome Fragment Assembly: The Case of Assembling Zymomonas mobilis ZM4 Sequences.
Cholhee Jung, Jin Young Choi, Hyun Seok Park, Jeong Sun Seo
1Department of Computer Science and Engineering,Korea University, Seoul 136-701, Korea.
2Institute of Bioinformatics, Macrogen Corp., Seoul 153-023, Korea.
3Department of Computer Science and Engineering,Ewha University, Seoul 120-750, Korea.
4School of Medicine, Seoul National University, Seoul 151-742, Korea.
Abstract
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.
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