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 http://www.expasy.org/sprot
 * 3) Type in gp120 + envelope protein + HIV-1 in the search windown and then click the search button. A list of relevant protein sequences should be shown.
 * 4) Click the link to your protein sequence that's relevant to your query [[Image:Picture_8.png]]
 * 5) Scroll to the bottom right of the screen and click on the FASTA format link [[Image:FASTA.png]]

Ch 4:
Deciphering the EGFR Swiss-Prot entry:


 * 1) Go to http://www.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. Also included are the references, comments, keywords, features, and the sequence. [[Image:EPGF.png]]
 * 4) Do the same thing for gp120 protein accession number P04578.

Ch 5:
'''ORFing your DNA sequence
 * 1) Go to www.ncbi.nlm.nih.gov/gorf/gorf.html
 * 2) Go to biology workbench and retrieve sequence in txt format from one of your subjects
 * 3) Copy and paste the sequence in the input box
 * 4) Click the OrfFind button [[Image:orf.png]]
 * 5) To examine the ORF's more closely click, click the corresponding rectangle in the graphical display
 * 6) Compare this ORF to the ORF to gp120 protein you found earlier [[Image:Gp120orf.png]]

Ch 6:
Predicting the Main Physio-chemical properties of a protein
 * 1) Go to http://www.expasy.org/tools/#primary
 * 2) Click the ProtParam link near the top
 * 3) Enter your sequence from the gp120 protein by copy and pasting the sequence or entering the accession number
 * 4) Click the compute parameters button. Then press submit and proceed to analysis
 * 5) Save results: [[Image:Protparam.png]]

Looking for transmembrane segments
 * 1) Go to www.expasy.org/cgi-bin/protscale.pl. The ProtScale page duly appears.
 * 2) Enter the accession number  P04578 in the small search box.
 * 3) Scroll down and select the radio button next to Hphob./Kyte & Doolittle. You do this because ProtScale gives you a large rannge of properties to choose and test on your protein. This one is appropriate for predicting transmembrane helices.
 * 4) From the Window Size pull-down menu, choose #19
 * 5) Press submit button at the bottom of the page
 * 6) Enter the range of analysis
 * 7) Click the submit button[[Image:protparam.png]]
 * 8) Click Image in GIF format at the bootm of the page and save the file