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