Team:CBNU-Korea/Method GOD

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<img src="https://static.igem.org/mediawiki/2011/c/c1/Synb_Project_Abstract.png">
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To design the Synthetic Minimal Chromosome of a bacterium, that the information on essential genes, such as direction, position, length and function, is essential. In addition a new analyzing method which calculates the distance between replication origin and each essential gene (DTO; Distance to origin) in each species, and provides the number of essential genes within 10 percent of total genome size are required. Using this method, we confirmed a distribution of essential genes in each organism.<br>
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<B>Essential Gene?</B><br>
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In this study the information of essential genes will be obtained from DEG (Database of Essential Genes). We will re-group essential genes by COG distribution for construction of our database which is connected to a software named GOD (Genome Organization Database & Designer).
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All of the organism must have essential genes for surviving in environment. All essential genes have specific essential biological function such as replication, transcription, translation and metabolism, etc. The essential gene is an element of genome, also life.<br><br>
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<B>what we try to, with essential genes? </B><br>
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If user wants to have characterized microbes, user should has to know what genome of the organism has, and then should design the microbe genome. For characterized alive microbes, they must have several essential genes. So we try to develop software that can help user design artificial genome or chromosome with several essential genes which is in our essential gene database.<br><br>
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<B>Data Parsing</B><br>
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Stored MySQL Database Using Java & BioJava <br>
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<img src="https://static.igem.org/mediawiki/2011/0/01/Synb%EC%97%B0%EA%B5%AC%EB%82%B4%EC%9A%A91.png" width="468px" height="446px"><br><br>
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<B>Data Processing</B><br>
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<img src="https://static.igem.org/mediawiki/2011/d/de/SynB%EC%97%B0%EA%B5%AC%EB%82%B4%EC%9A%A92.png" width="567px" height="573px"><br><br>
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<B>Making Essential genes Pool</B><br>
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<img src="https://static.igem.org/mediawiki/2011/b/b1/Synb%EC%97%B0%EA%B5%AC%EB%82%B4%EC%9A%A93.png"><br><br>
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<B>Analogy of Essential genes</B><br>
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If the analysis method of 15 species of DEG is applied, other essential genes in many organisms which are not finished the Genome project could be analogized by using the information of the analogized essential genes in DEG.<br>
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<br>
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<B>Analysis of essential genes</B><br>
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The study on the Essential gene’s position of microorganism species of 1500 about origin. We analysis NC file’s various parameters (Strand, Direction, COG, EG, DistToOri, etc.) to study distribution of essential gene. The Strand, Direction, COG, EG, DistToOri was used from the various parameters.<br><center><img src="https://static.igem.org/mediawiki/2011/7/71/Synb_GOD_pic1.png"></center><br><br>
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<B>GOD,Genome Organization database & Designer</B><br>
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<img src="https://static.igem.org/mediawiki/2011/5/53/SynB%EC%97%B0%EA%B5%AC%EB%82%B4%EC%9A%A94.png" width="567px" height="412px"><br>
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<img src="https://static.igem.org/mediawiki/2011/a/aa/Synb_GOD_pic2.png"><br>
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Latest revision as of 20:53, 5 October 2011


Essential Gene?
All of the organism must have essential genes for surviving in environment. All essential genes have specific essential biological function such as replication, transcription, translation and metabolism, etc. The essential gene is an element of genome, also life.

what we try to, with essential genes?
If user wants to have characterized microbes, user should has to know what genome of the organism has, and then should design the microbe genome. For characterized alive microbes, they must have several essential genes. So we try to develop software that can help user design artificial genome or chromosome with several essential genes which is in our essential gene database.

Data Parsing
Stored MySQL Database Using Java & BioJava


Data Processing


Making Essential genes Pool


Analogy of Essential genes
If the analysis method of 15 species of DEG is applied, other essential genes in many organisms which are not finished the Genome project could be analogized by using the information of the analogized essential genes in DEG.

Analysis of essential genes
The study on the Essential gene’s position of microorganism species of 1500 about origin. We analysis NC file’s various parameters (Strand, Direction, COG, EG, DistToOri, etc.) to study distribution of essential gene. The Strand, Direction, COG, EG, DistToOri was used from the various parameters.


GOD,Genome Organization database & Designer

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