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Team:Glendale CC AZ/Protocols/Bioinformatics
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Revision as of 03:01, 23 September 2013
Glendale Community College Arizona
Protocols
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.
