1. HIV Project -Matt Hagen

2. The Problem Are there any DNA sequences in common between HIV and human genomes? HIV-1, complete genome, chimeric clone AF033819.3HIV-1, complete genome UCSC Human genome, March 2006 AssemblyUCSC

3. What’s been done

4. Determine if the matches found are significant Are these matches due to chance?

5. Current Problem Calculate expected outcomes o Find all unique sequences in each chromosome of length 16 Obtain frequencies for all unique sequences Chi Squared Analysis?

6. Unique Sequences

7. Current Problem How are the matches distributed along the HIV genome? Distributed evenly Distribution is not equal Distribution is in clusters

8. – Distribution of sequence matches across the HIV genome, overlaps removed

9. Distribution of Matches Are areas on the HIV Genome more represented than others?

13. Future Work Why are some areas more represented than others? What is the biological significance of these areas? Where are these sequences found in the human genome? Nice graphic output of matches...