Isaiah M. Castaneda Week 4

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1. What is your question?

Which subjects did show evidence of predominance of a single strain and do these subjects share something in common?

2. Make a prediction (hypothesis) about the answer to your question before you begin your analysis.

The subjects may all be in the same category of progression. Therefore, the predominance of one strain may be unique to or indicative of a particular level of progression.

3. Which subjects, visits, and clones will you use to answer your question?

Subjects 2, 3, 4, 6, 12, and 13 will be used. Ideally, all of their visits and clones will be used to help build and use phylogenetic trees. However, if a tool cannot be found which could handle >50 sequences, we will narrow the number down to include select groups of sequences from early visits, later visits, and visits in between.

4. Justify why you chose the subjects, visits, and clones you did.

A method of comparing ratios of unique sequences:number of sequences for the subjects whose trees were not shown in the paper was used to gather suspects for who the 5 that we are searching for might have been. The 6 subjects listed above had the lowest ratios and therefore lowest amount of distinct sequences. So far, they are the main candidates for those that may have had a predominant strain. Creation of phylogenetic trees for these subjects may help to filter out the 6th unwanted person.