Isaiah M. Castaneda Week 5
After opening up last week's data, it was time to get to work. Based on last week's findings, subjects 2, 3, 4, 6, 12, and 13 would be explored. The goal of last week was to find the 5 subjects whose HIV patterns indicated predominance of a single strain at any point during the experiment. Using ratios of unique:total sequences, we only narrowed it down to 6 subjects. Hopes were that by constructing phylogenetic trees, it would be more clear which subject did not have a predominant strain. The sequences from all the visits of the desired subjects (taken from http://bioquest.org/bedrock/problem_spaces/hiv/nucleotide_sequences.php) was uploaded to the Biology WorkBench. In addition to these, subject number 5 was added as well to make sure that the trees would be similar to the ones presented in the paper. Multiple sequence alignments were run on each of the 7 subjects and from those alignments, rooted phylogenetic trees were created (same style as the trees from the article). First, subject 5's phylogenetic tree was created to compare to the tree from the paper. As one may see, there is a decent resemblance.
Therefore, there should be no major problem using trees created by Workbench to compare & contrast with the trees from Markham et al article. Trees were then made for the other 6 subjects which will be shown in our slideshow presentation.