• Journal of Microbiology and Biotechnology
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• v.10 no.3
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• pp.405-409
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• 2000

We have studied the genome of an obligately commensal thermophile, Symbiobacterium toebii. The chromosome was extracted from pure cultures of S. toebii recently established. Total DNA of S. toebii was resolved by pulsed-field gel electrophoresis (PFGE) into discrete numbers of fragments by digenstion with the endonuclease SspI, SpeI, XbaI, and HpaI. Estimated sizes of fragments produced by the four enzymes and their sum consistently yielded a total genome size of 2.8 Mb. Because restriction endonucleases NotI and SwaI, recognizing 8 bp, released too many fragments, these enzymes could not be used for the estimation of the genome size. Considering no mobility of undigested genome under PFGE, the genome of S. toebii appears to be circular. The presence of extrachromosomal DNA in S. toebii was excluded by the results of the conventional 1% agarose gel electrophoresis and the field inversion gel electrophoresis of undigested S. toebii DNA.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.04a
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• pp.22-23
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• 2005

• Genomics & Informatics
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• v.20 no.1
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• pp.3.1-3.10
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• 2022

The recent development of whole-genome sequencing technologies paved the way for understanding the genomes of microorganisms. Every whole-genome sequencing (WGS) project requires a considerable cost and a massive effort to address the questions at hand. The final step of WGS is data analysis. The analysis of whole-genome sequence is dependent on highly sophisticated bioinformatics tools that the research personal have to buy. However, many laboratories and research institutions do not have the bioinformatics capabilities to analyze the genomic data and therefore, are unable to take maximum advantage of whole-genome sequencing. In this aspect, this study provides a guide for research personals on a set of bioinformatics tools available online that can be used to analyze whole-genome sequence data of bacterial genomes. The web interfaces described here have many advantages and, in most cases exempting the need for costly analysis tools and intensive computing resources.

• BMB Reports
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• v.37 no.1
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• pp.75-82
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• 2004

Recent years saw a dramatic increase in genomic and proteomic data in public archives. Now with the complete genome sequences of human and other species in hand, detailed analyses of the genome sequences will undoubtedly improve our understanding of biological systems and at the same time require sophisticated bioinformatic tools. Here we review what computational challenges are ahead and what are the new exciting developments in this exciting field.

• 대한생식의학회:학술대회논문집
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• 2004.06a
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• pp.75-75
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• 2004

• 대한생식의학회:학술대회논문집
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• 2006.11a
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• pp.148-148
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• 2006

• The Korea Genome Conference
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• 2005.09a
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• pp.33-33
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• 2005

• Microbiology and Biotechnology Letters
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• v.51 no.3
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• pp.306-308
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• 2023

This research presents the whole-genome sequence of Enterobacter asburiae strain IK3, which was isolated from the rhizosphere soil of soybean (Glycine max). The genome of the strain is composed of a single chromosome with 4 plasmids, total size of 5,084,040 bp, and the GC content is 55.5%.

• Genomics & Informatics
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• v.7 no.3
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• pp.159-162
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• 2009

Human personal genome sequencing can be done with high efficiency by aligning a huge number of short reads derived from various next generation sequencing (NGS) technologies to the reference genome sequence. One of the major obstacles is the incompleteness of human reference genome. We tried to analyze the effect of hidden gene duplication on the NGS data using the known example of hydin gene. Hydin2, a duplicated copy of hydin on chromosome 16q22, has been recently found to be localized to chromosome 1q21, and is not included in the current version of standard human genome reference. We found that all of eight personal genome data published so far do not contain hydin2, and there is large number of nsSNPs in hydin. The heterozygosity of those nsSNPs was significantly higher than expected. The sequence coverage depth in hydin gene was about two fold of average depth. We believe that these unique finding of hydin can be used as useful indicators to discover new hidden multiplication in human genome.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.221-228
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• 2003

This paper presents a novel method that can identify the individual's haplotype from the given genotypes. Because of the limitation of the conventional single-locus analysis, haplotypes have gained increasing attention in the mapping of complex-disease genes. Conventionally there are two approaches which resolve the individual's haplotypes. One is the molecular haplotypings which have many potential limitations in cost and convenience. The other is the in-silico haplotypings which phase the haplotypes from the diploid genotyped populations, and are cost effective and high-throughput method. In-silico haplotyping is divided into two sub-categories - statistical and computational method. The former computes the frequencies of the common haplotypes, and then resolves the individual's haplotypes. The latter directly resolves the individual's haplotypes using the perfect phylogeny model first proposed by Dan Gusfield [7]. Our method combines two approaches in order to increase the accuracy and the running time. The individuals' haplotypes are resolved by considering the MLE (Maximum Likelihood Estimation) in the process of computing the frequencies of the common haplotypes.