• Korean Journal of Agricultural Science
• /
• v.31 no.1
• /
• pp.35-44
• /
• 2004

In this study, the automatic system exchanging well-plates was developed as a basic stage of the genome project. The developed system consisted of the plate fixing well-plates, the well-plate cassette, the head to move a well-plate from the well-plate cassette to the plate fixing well-plates before genome work or from the plate to the cassette after the work, the manipulator to move the head on the X, Y and Z axes and the control system. The performance test to exchange well-plates with the robotic system developed was carried out. The time to set an well-plate from the well-plate cassette onto the board fixing well-plates was 55 seconds and the time for 9 ones was 8 minutes and 15 seconds. It took 57 seconds to move a well-plate from the board to the cassette and 8 minutes and 33 seconds for 9 ones.

• Journal of the Korean Society of International Agriculture
• /
• v.23 no.5
• /
• pp.560-569
• /
• 2011

In Japan, plant genomics research is mainly leaded by the national research institutes. The various structural studies such as rice genome has allowed researchers to analyze useful traits, and to focus their commercialization. With aims to facilitate structural and functional study in plant genome, NIAS (National Institute of Agrobiological Sciences) constructed Poaceae genome DB and RIKEN (Rikagaku Kenkyusho) built DB for Arabidopsis genome and plant full-length cDNA. NIG (National Institute of Genetics) constructed a national biological resources DB (National Bio Resource Project). This compiling DB provides a variety of genome-related research materials for researchers in the field. Recently, as an effort to resolve global issues of food supply and environmental problems, New Agri-genome Project has been performed aiming to develop an innovative agricultural technologies for the quantity, disease resistance and identifying useful genes related to environmental problems. In addition, in order to improve agricultural productivity in developing countries, JIRCAS assisted technical supports for the plant genome research and developed NERICA rice, which is suitable for African area. Such these approaches are expected to contribute to solving the global issues about food, energy and environment in the world.

• 대한치주과학회:학술대회논문집
• /
• 2005.11a
• /
• pp.226-227
• /
• 2005

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

• KOGO NEWS
• /
• v.3 no.1
• /
• pp.6.1-6.1
• /
• 2003

• Journal of Plant Biotechnology
• /
• v.33 no.3
• /
• pp.153-160
• /
• 2006

Brassica rape is an important species used as a vegetable, oil, and fodder worldwide. It is related phylogenically to Arabidopsis thaliana, which has already been fully sequenced as a model plant. The 'Multinational Brassica Genome Project (MBGP)'was launched by the international Brassica community with the aim of sequencing the whole genome of B. rapa in 2003 on account of its value and the fact that it has the smallest genome among the diploid Brassica. The genome study was carried out not only to know the structure of genome but also to understand the function and the evolution of the genes comprehensively. There are two mapping populations, over 1,000 molecular markers and a genetic map, 2 BAC libraries, physical map, a 22 cDHA libraries as suitable genomic materials for examining the genome of B. rapa ssp. pekinensis Chinese cabbage. As the first step for whole genome analysis, 220,000 BAC-end sequences of the KBrH and KBrB BAC library are achieved by cooperation of six countries. The results of BAC-end sequence analysis will provide a clue in understanding the structure of the genome of Brassica rapa by analyzing the gene sequence, annotation and abundant repetitive DHA. The second stage involves sequencing of the genetically mapped seed BACs and identifying the overlapping BACs for complete genome sequencing. Currently, the second stage is comprises of process genetic anchoring using communal populations and maps to identify more than 1,000 seed BACs based on a BAC-to-BAC strategy. For the initial sequencing, 629 seed BACs corresponding to the minimum tiling path onto Arabidopsis genome were selected and fully sequenced. These BACs are now anchoring to the genetic map using the development of SSR markers. This information will be useful for identifying near BAC clones with the seed BAC on a genome map. From the BAC sequences, it is revealed that the Brassica rapa genome has extensive triplication of the DNA segment coupled with variable gene losses and rearrangements within the segments. This article introduces the current status and prospective of Korea Brassica Genome Project and the bioinformatics tools possessed in each national team. In the near future, data of the genome will contribute to improving Brassicas for their economic use as well as in understanding the evolutional process.

• Genomics & Informatics
• /
• v.6 no.4
• /
• pp.166-172
• /
• 2008

A multitude of protein-coding sequence variations (CVs) in the human genome have been revealed as a result of major initiatives, including the Human Variome Project, the 1000 Genomes Project, and the International Cancer Genome Consortium. This naturally has led to debate over how to accurately assess the functional consequences of CVs, because predicting the functional effects of CVs and their relevance to disease phenotypes is becoming increasingly important. This article surveys and compares variation databases and in silico prediction programs that assess the effects of CVs on protein function. We also introduce a combinatorial approach that uses machine learning algorithms to improve prediction performance.

• Proceedings of the Korean Society of Life Science Conference
• /
• 2003.10a
• /
• pp.14-27
• /
• 2003

The genomes of Arabidopsis and rice have been fully sequenced. Genomic sequencing provides global information about genome structure and organization. A comprehensive research account of our recent studies conducted on genome painting, comparative genomics and genome fusion is provided in order to project the prospects of plant cytogenetic research in post-genomics era. Genome analysis by GISH using genome painting is demonstrated as an excellent means suitable for visualization of a whole genome, since total genomic DNA representing the overall molecular composition of the genome is used as a probe. FISH on extended DNA fibers has been developed for high-resolution FISH and has contributed to determining the copy number and order of genes. We have also mapped a number of genes involving starch synthesis on wheat chromosomes by FISH and compared the position of these genes on linkage map of rice. Macro synteny between wheat and rice can be observed by comparing the location of these genes in spite of the fact that the size of DNA per chromosome differs by 20 fold in two. Moreover, to approach our goal towards making bread and udon noodles from rice flour in future by incorporating bread making and the noodle qualifies in rice, we have been successful in introducing large genomic DNA fragments containing agronomically important genes of wheat into a rice by successive introduction of large insert BAC clones, there by expanding genetic variability in rice. We call this method genome fusion.

• Genomics & Informatics
• /
• v.7 no.3
• /
• pp.178-180
• /
• 2009

A few bioinformatics tools have been used to find out conserved regions as probes. We have developed a system based on a heuristic method with web interfaces to find out conserved regions against microbial genomes. The system runs in real time by using relative entropy in limited narrow regions and detecting similar regions between pair regions with local alignment. The system could be useful to find out conserved regions as genome-wide scale.

• Journal of Scientific & Technological Knowledge Infrastructure
• /
• s.3
• /
• pp.34-39
• /
• 2000

프로테옴의 연구가 앞으로 많은 지원을 받을 것을 예상되는데 과연 우리는 프로테움의 결과를 기다리면 되는 것일까? 그렇지 않다. 오히려 프로테옴 연구와 병행하여 실제 살아 있는 세포.장기.개체에서 일어나는 유전정보의 발현을 더 중요하게 연구해야 한다고 생각한다. 그런 필요에 의하여 생긴 개념이 바로 Physiome(피지옴)이다.