• Journal of Korea Multimedia Society
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• v.7 no.3
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• pp.408-417
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• 2004

Genome analysis process requires several steps of various software analysis tools. We propose WGAT(Web-based Genome Analysis Tool), which combines several tools for gene analysis and provides a graphic user interface for users. Software tools related to gene analysis are based on Linux or Unix oriented program, which is difficult to install and use for biologists. Furthermore, files generated from gene analysis frequently require manual transformation for next step input file. Web-based tools which are recently developed process orily one sequence at a time. So it needs many repetitive processes to analyze large size data file. WGAT is developed to support Web-based genome analysis for easy use as well as fast service for users. Whole genome data analysis can be done by running WGAT on Linux server and giving sequence data files with various options. Therefore many steps of the analysis can be done automatically by the system. Simulation shows that WGAT method gives 20 times faster analysis when sequence segment is one thousand.

• Journal of Microbiology and Biotechnology
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• v.25 no.10
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• pp.1599-1605
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• 2015

The development of rapid and efficient genome sequencing methods has enabled us to study the evolutionary background of bacterial genetic information. Here, we present comparative genomic analysis of 17 Streptomyces species, for which the genome has been completely sequenced, using the pan-genome approach. The analysis revealed that 34,592 ortholog clusters constituted the pan-genome of these Streptomyces species, including 2,018 in the core genome, 11,743 in the dispensable genome, and 20,831 in the unique genome. The core genome was converged to a smaller number of genes than reported previously, with 3,096 gene families. Functional enrichment analysis showed that genes involved in transcription were most abundant in the Streptomyces pan-genome. Finally, we investigated core genes for the sigma factors, mycothiol biosynthesis pathway, and secondary metabolism pathways; our data showed that many genes involved in stress response and morphological differentiation were commonly expressed in Streptomyces species. Elucidation of the core genome offers a basis for understanding the functional evolution of Streptomyces species and provides insights into target selection for the construction of industrial strains.

• Proceedings of the PSK Conference
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• 2002.04a
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• pp.94-95
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• 2002

• Genomics & Informatics
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• v.3 no.2
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• pp.73-76
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• 2005

The comparative analysis of the human and primate genomes including the chimpanzee can reveal unique types of information impossible to obtain from comparing the human genome with the genomes of other vertebrates. PrimateDB is an open depository server that provides primate genome information for the comparative genome research. The database also provides an easy access to variable information within/between the primate genomes and supports analyzed information, such as annotation and retroelements and phylogeny. The comparative analyses of more primate genomes are also being included as the long-term objective.

• Genomics & Informatics
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• v.2 no.4
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• pp.180-183
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• 2004

Comparative Statistic Module(CSM) provides more reliable list of significant genes to genomics researchers by offering the commonly selected genes and a method of choice by calculating the rank of each statistical test based on the average ranking of common genes across the five statistical methods, i.e. t-test, Kruskal-Wallis (Wilcoxon signed rank) test, SAM, two sample multiple test, and Empirical Bayesian test. This statistical analysis module is implemented in Perl, and R languages.

• The Korea Genome Conference
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• 2006.09a
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• pp.50-50
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• 2006

• The Korea Genome Conference
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• 2006.09a
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• pp.48-48
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• 2006

• The Korea Genome Conference
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• 2005.09a
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• pp.38-38
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• 2005

• The Korea Genome Conference
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• 2005.09a
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• pp.42-42
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• 2005

• The Korea Genome Conference
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• 2005.09a
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• pp.74-74
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• 2005