Bobak Seddighzadeh Week 8

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:

1. 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.
2. Go to ww.expasy.org/sprot/
3. Type in gp120 + envelope protein + HIV-1
4. Click the link to your protein sequence that's relevant to your query
5. Scroll to the bottom right of the screen and click on the FASTA format link

Ch 4:

Deciphering the EGFR Swiss-Prot entry:

1. Go to ww.expasy.org/sprot/
2. Type in the Swiss Prot ID P00533 in the search window at the top of the page
3. Click the go button to reveal the general information about the entry and name and origin of the protein

Ch 5:

ORFing your DNA sequence

1. Go to www.ncbi.nlm.nih.gov/gorf/gorf.html

1. Convert your DNA sequences into protein sequences. The first step to do this requires us to find the open reading frame (ORF) of the DNA sequence. We decided to use the same set of subjects, clones, and visits from the project that Kris Chin and I did during week six.
   1. Point your broswer to ww.