J'aime C. Moehlman's Week 9

HIV Structure Research Project

 * Our Question: Will there be specific differences between the protein sequences in subject 10 and 12 that results in different protein structures, which changes the function of the virus?
 * We chose subjects 10 and 12; we chose them because their CD4 T cell rates had the widest range.
 * We chose subject 10 because it had the largest decrease in CD4 T cell counts; of the 3 rapid progressors in our previous project 10 had the most visits and we chose it because we felt that would have the best data.
 * We chose subject 12 because it had a an average rate of CD4 T cell increase within the nonprogressors.
 * We chose all of the clones from visit 4 and 5 because both subjects were present and there are a total of 42 protein sequences.
 * Include table 1 from the original markham paper in powerpoint.

Methods

 * Run a multiple sequence alignment for subjects 10 and 12 (all clones from visits 4 and 5).
 * Also, run a box shade color coded plot in order to more clearly see where the differences are located between the two subjects.
 * From the boxshade we determined which amino acids were predominantly different between the two groups. We picked a clone from each subject to be the representative for PROSITE:
 * Subject 10; visit 4 clone 2.
 * Subject 12; visit 4 clone 4.

[[Media:Bioinformatics HIV Structure Project1-final.ppt|Structure Project]]