Team:Glendale CC AZ/Protocols/Bioinformatics

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== Searching for Homolog Genes ==
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<img style="border: 0px solid ; width: 50px; height: 40px;" alt="iGEM" src="http://s21.postimg.org/ff5nkjy9v/IGEM_basic_Logo_stylized.png" align="left">
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<h4>Glendale Community College Arizona<img
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style="width: 200px; height: 58px;" alt="GCC"
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  <h2><p>Protocols</p></h2><img style="border: 0px solid ; width: 400px; height: 200px;" alt="iGEM" src="https://static.igem.org/mediawiki/igem.org/1/19/Tubes2GCC.JPG" align="right">
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<a href="https://2013.igem.org/Team:Glendale_CC_AZ/Protocols/GrowthCurve">Growth Curve  Assay</a></p>
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<a href="https://2013.igem.org/Team:Glendale_CC_AZ/Protocols/NaCl">NaCl Growth Curve Assay</a></p>
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<a href="https://2013.igem.org/Team:Glendale_CC_AZ/Protocols/SurivalGrowth">Survival Growth  Assay</a></p>
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<a href="https://2013.igem.org/Team:Glendale_CC_AZ/Protocols/AlkalineLysis">Alkaline Lysis Plasmid Miniprep </a></p>
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<a href="https://2013.igem.org/Team:Glendale_CC_AZ/Protocols/RestrictionDigest">Restriction Digest</a></p>
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<a href="https://2013.igem.org/Team:Glendale_CC_AZ/Protocols/DNAIsolation">DNA Isolation</a></p>
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<a href="https://2013.igem.org/Team:Glendale_CC_AZ/Protocols/Bioinformatics">Bioinformatics</a></p>
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<a href="https://2013.igem.org/Team:Glendale_CC_AZ/Protocols/Ligation">Ligation</a></p>
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<a href="https://2013.igem.org/Team:Glendale_CC_AZ/Protocols/Transformation">Transformation</a></p>
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=== Searching for Homolog Genes ===
Website: http://img.jgi.doe.gov/cgi-bin/edu/main.cgi
Website: http://img.jgi.doe.gov/cgi-bin/edu/main.cgi
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5. Scroll through the chart displayed until you find the genome you are searching for, click the "select" box at the far left, then click "Add selections to gene cart".
5. Scroll through the chart displayed until you find the genome you are searching for, click the "select" box at the far left, then click "Add selections to gene cart".
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6. Repeat this process to compare genes of interest.  
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6. Repeat this process with all genes of interest.
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7. If you're interested in comparing genes of interest, click on the "Analysis Cart" tab at the top of the page, then click on "gene". All genes that have been added to the gene cart will appear here. You can view and compare chromosome maps, sequence alignments, functions, and/or gene neighborhoods.
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=== Designing Primers ===
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Once genes of interest have been added to the gene cart you can begin to design primers.
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1. From the gene cart, click on the "Gene ID" of the gene you are interested in created a primer for.
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2. Scroll down under the Gene Information section of the page. When you reach the "DNA coordinates" column on the table provided click on the number of base pairs. This is a link that will take you to the gene sequence.
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3. Copy the sequence provided.  
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4. Open a new tab and enter the following url: http://primer3.ut.ee/
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== Designing Primers ==
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5. Paste the gene sequence into the open box provided at the top of the page. Then click "Pick Primers" and all relevant info is provided along with the forward and reverse primers for the sequence you provided.

Latest revision as of 02:36, 28 September 2013

iGEM

Glendale Community College ArizonaGCC

Protocols

iGEM Growth Curve Assay

NaCl Growth Curve Assay

Survival Growth Assay

Alkaline Lysis Plasmid Miniprep

Restriction Digest

DNA Isolation

Bioinformatics

Ligation

Transformation

Searching for Homolog Genes

Website: http://img.jgi.doe.gov/cgi-bin/edu/main.cgi

1. Click "find genes".

2. Change filter setting to search by "Locus Tag", enter the locus tag, and click "go".

3. Scroll to the bottom of the screen and click "Homolog Display".

4. Change "Homolog Selection" to "Top IMG Homolog Hits".

5. Scroll through the chart displayed until you find the genome you are searching for, click the "select" box at the far left, then click "Add selections to gene cart".

6. Repeat this process with all genes of interest.

7. If you're interested in comparing genes of interest, click on the "Analysis Cart" tab at the top of the page, then click on "gene". All genes that have been added to the gene cart will appear here. You can view and compare chromosome maps, sequence alignments, functions, and/or gene neighborhoods.

Designing Primers

Once genes of interest have been added to the gene cart you can begin to design primers.

1. From the gene cart, click on the "Gene ID" of the gene you are interested in created a primer for.

2. Scroll down under the Gene Information section of the page. When you reach the "DNA coordinates" column on the table provided click on the number of base pairs. This is a link that will take you to the gene sequence.

3. Copy the sequence provided.

4. Open a new tab and enter the following url: http://primer3.ut.ee/

5. Paste the gene sequence into the open box provided at the top of the page. Then click "Pick Primers" and all relevant info is provided along with the forward and reverse primers for the sequence you provided.

Retrieved from "http://2013.igem.org/Team:Glendale_CC_AZ/Protocols/Bioinformatics"