Bobak Seddighzadeh Week 8: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
(→Ch 5:) |
No edit summary |
||
Line 29: | Line 29: | ||
#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 | ||
#Click the OrfFind button [[Image: | #Click the OrfFind button [[Image:orf.png]] |
Revision as of 13:09, 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 Expasy
- 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 Expasy
- 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