Matthew K. Oki Individual Journal 4

Matthew K. Oki I.J. Week 4

Methods & Results

1. The formal methods were followed from Activity 2 of the Exploring HIV Evolution

Activity 2, Part 1

1. Download the provided sequences of subjects 10-15 from BIOL368/F16:Week 4
   • Upload these sequences into the Biology Workbench
2. Run the multiple sequence alignment for the selected subjects and clones
   • The subjects & clones below were used:

1. • The output results in the following uprooted tree:

Activity 2, Part 2

1. Three individual subjects were run through multiple sequence alignment
   • Each nucleotide difference (S) was denoted by the absence of a star as shown below with Subject 15:

1. Theta was then calculated:
   • Theta is an estimate of the average pairwise genetic distance
   • The equation from Exploring HIV Evolution is given below:

1. Min and Max difference were calculated:
   • One subject's clones were selected and run through the same multiple sequence alignment
   • Click on "Import Alignments"
   • Go to the "Alignment Tool" tab
   • Run a "Clustaldist" test
   • A matrix is produced as shown below:

• The highest and lower numbers in this matrix were multiplied by the length of sequence
  • Rounding these numbers to the nearest integer gives us maximum and minimum respectively
• This was performed for all 3 of the subjects picked above with the results in the table below:

• Finally, the min and max were calculated from a comparison of two subjects:
  • The table below gives the results of three comparisons:

Defining Research Project

Question

Is there a genetic difference in HIV-1 in patients who contracted the virus sexually or by intravenous injection?

Hypothesis

We hypothesize that there will not be a genetic difference in HIV-1 in patients who contracted the virus sexually or by intravenous injection

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