Team:CBNU-Korea/Methods/Com

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????
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<br><font color=white size="4" face="Tahoma">
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<b>1. DoriC DataBase</b><br>
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1-1. Parse oriC region of Genome from DoriC site.<br>
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<img src="https://static.igem.org/mediawiki/2011/c/c1/Synb_COM_002.png"><br>
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1-2. Calculate Terminus from Parced Data<br>
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<img src="https://static.igem.org/mediawiki/2011/d/db/Synb_COM_003.png"><br>
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<br>
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<b>2. Essential Gene Pool</b><br>
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2-1. Parse 15 species essential gene from DEG site.<br>
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<img src="https://static.igem.org/mediawiki/2011/7/76/Synb_COM_006.png"><br>
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<img src="https://static.igem.org/mediawiki/2011/e/e1/Synb_COM_007.png"><br>
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2-2. Get data(Strand, StartPoint, EndPoint, etc) from every NC files.<br>
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2-3. base on these data, calculate Distance To the Origin(DTO), Scale, Direction, etc.<br>
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- DTO <br>
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<img src="https://static.igem.org/mediawiki/2011/a/ab/Synb_iDTO_1case.png">
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<img src="https://static.igem.org/mediawiki/2011/5/5b/Synb_iDTO_2case.png"><br>
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<img src="https://static.igem.org/mediawiki/2011/2/26/Synb_iDTO_3case.png"><br>
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- Scale <br>
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<img src="https://static.igem.org/mediawiki/2011/1/1c/Synb_COM_008.png"><br>
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<br>
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<b>3. Distribute Essential Gene Pool By COG to compile statistics.</b><br>
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3-1. make DB of deg15_eg_cog that named table by EGName and COG.(ex. Acinetobacter_a, Acinetobacter_b, ...)<br>
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<center>
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<img src="https://static.igem.org/mediawiki/2011/7/76/Acinetobacter_of_Deg15_cog.png">
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</center>
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<br>
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<br>
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3-2. make DB of deg15_cog that named table by COG.(ex. a,b,c......z)<br>
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<center>
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<img src="https://static.igem.org/mediawiki/2011/8/89/Acinetobacter_of_Deg15_eg_cog.png">
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</center>
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<br>
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<br>
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<b>4. Analysis the data.</b><br>
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4-1. Analysed DB of deg15.<br>
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<br>
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<b>5. 1080 species DB</b><br>
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5-1. Download NC files from ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ <br>
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5-2. First step is to check whether a data is existing or not by matching  individually between NC file and DoriC DB.<br>
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5-3. Second step is that if there is a data, then confirm whether a GenomeSize is same between NC file and DB.<br>
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5-4. last step. if it is same, the data goes to DB.<br>
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<br>
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<b>6. Discover which things are in common between 15 species essential genes.</b><br>
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6-1. Find genes that COG Number, strand, scale, and Direction are same from Distributed Essential Gene Pool by COG.<br>
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<br>
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Latest revision as of 21:10, 5 October 2011


1. DoriC DataBase
1-1. Parse oriC region of Genome from DoriC site.

1-2. Calculate Terminus from Parced Data


2. Essential Gene Pool
2-1. Parse 15 species essential gene from DEG site.


2-2. Get data(Strand, StartPoint, EndPoint, etc) from every NC files.
2-3. base on these data, calculate Distance To the Origin(DTO), Scale, Direction, etc.
- DTO


- Scale


3. Distribute Essential Gene Pool By COG to compile statistics.
3-1. make DB of deg15_eg_cog that named table by EGName and COG.(ex. Acinetobacter_a, Acinetobacter_b, ...)


3-2. make DB of deg15_cog that named table by COG.(ex. a,b,c......z)


4. Analysis the data.
4-1. Analysed DB of deg15.

5. 1080 species DB
5-1. Download NC files from ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/
5-2. First step is to check whether a data is existing or not by matching individually between NC file and DoriC DB.
5-3. Second step is that if there is a data, then confirm whether a GenomeSize is same between NC file and DB.
5-4. last step. if it is same, the data goes to DB.

6. Discover which things are in common between 15 species essential genes.
6-1. Find genes that COG Number, strand, scale, and Direction are same from Distributed Essential Gene Pool by COG.

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