Salomon Garcia: Week 9

Formulating our question for the next project and this is what we as a group came up with:

Sequence Alignment

 * For this experiment we will be using the Markham et al Paper and we will also be using the Stanfield et al paper. These are the two links for them
 * [[Media:Sdarticle.pdf| Stanfield Article]]
 * 1) Paper1 pmid=9770526
 * 1) Paper1 pmid=9770526


 * The sequence alignment was done for each of the Subjects in this case it was for subject 12 and subject 13, sequence alignment was done and this is what was shown for both of the subjects. The sequence alignment was done by using Biology WorkBench. These are the images that are seen:



Matricies

 * Once the sequence alignment was done then a ClustalDist Matrix was ran in order to get the max for each of the clones and there particular visits and the matrix for both of the subjects is shown below.
 * min difference for subject 12= 1.045
 * max difference for subject 12= 7.03
 * min difference for subject 13= 1.045
 * max difference for subject 13= 7.03


 * After this matrices were done the next thing that was done was look at each subject and look at two visits at a time for example visits 3 and 4 and then 4 clones were gathered for these visits

Box Shade of Protein Sequences

 * For this portion of the project we sequences and we got a box shaded representation of our clones of Subject 12 and Subject 13 and this is what was seen:

Rooted and Unrooted Trees

 * Also from the sequence alignment of the 4 clones for each of the visits we get the rooted and unrooted trees and this is what it looks like.


 * For this experiment we decided on our article this is a Link to it:http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=78166
 * This is a the entire article in pdf file: [[Media:Article in pdf format.pdf|Article by Lei Chen]]
 * This is the link to the Presentation on HIV Structure:[[Media:Specific changes in the primary structure of rapid.ppt|PowerPoint Presentation Week 10]]