Bobak Seddighzadeh Week 8: Difference between revisions
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'''ORFing your DNA sequence | '''ORFing your DNA sequence | ||
#Go to www.ncbi.nlm.nih.gov/gorf/gorf.html | #Go to [http://www.ncbi.nlm.nih.gov/gorf/gorf.html www.ncbi.nlm.nih.gov/gorf/gorf.html] | ||
#Go to biology workbench and retrieve sequence in txt format from one of your subjects | #Go to biology workbench and retrieve sequence in txt format from one of your subjects | ||
#Copy and paste the sequence in the input box | #Copy and paste the sequence in the input box | ||
Line 36: | Line 36: | ||
#Go to [http://www.expasy.org/tools/#primary http://www.expasy.org/tools/#primary] | #Go to [http://www.expasy.org/tools/#primary http://www.expasy.org/tools/#primary] | ||
#Click the '''ProtParam''' link near the top | #Click the '''ProtParam''' link near the top | ||
#Enter your sequence from the gp120 protein by copy and pasting the sequence or entering the accession number | |||
#Click the compute parameters button. Then press submit and proceed to analysis | |||
# | # |
Revision as of 13:29, 9 March 2010
Question
The question that me and my partner decided to tackle is: What specific sequence changes in the V3 domain of HIV-1 play a role in altering its structure significantly enough to affect its function?
Procedure and Results:
Ch 2:
Retrieving protein sequences:
- First you must retrieve protein sequences form the web. You can use a host of sites such PubMed, but Bioinformatics for Dummies suggests using ExPASy instead because its a good site for protein information as well as being easy to use.
- Go to http://www.expasy.org/sprot
- Type in gp120 + envelope protein + HIV-1
- Click the link to your protein sequence that's relevant to your query
- Scroll to the bottom right of the screen and click on the FASTA format link
Ch 4:
Deciphering the EGFR Swiss-Prot entry:
- Go to http://www.expasy.org/sprot
- Type in the Swiss Prot ID P00533 in the search window at the top of the page
- Click the go button to reveal the general information about the entry and name and origin of the protein
- Do the same thing for gp120 protein. Type in
Ch 5:
ORFing your DNA sequence
- Go to www.ncbi.nlm.nih.gov/gorf/gorf.html
- Go to biology workbench and retrieve sequence in txt format from one of your subjects
- Copy and paste the sequence in the input box
- Click the OrfFind button
- To examine the ORF's more closely click, click the corresponding rectangle in the graphical display
- Compare this ORF to the ORF to gp120 protein you found earlier
Ch 6:
- Go to http://www.expasy.org/tools/#primary
- Click the ProtParam link near the top
- Enter your sequence from the gp120 protein by copy and pasting the sequence or entering the accession number
- Click the compute parameters button. Then press submit and proceed to analysis