Non: Week 6
The purpose of today's lab is to answer our hypothesis from last week: How does the location and identity of nucleotide differences observed in HIV clones in subjects with a similar slope of divergence affect virulence?
Subjects 2, 3, 5, 11, 13, 14 (2 from each progressor group; all have relatively similar slopes of divergence (less than 1))
four random clones from each subject's visit #1 and #4
For my portion of the presentation, I focused mainly on using Excel to analyze sequence data.
- I entered all of the sequence data from the noted subjects above from their first and fourth visits into Phylogeny.fr.
- I used the clustal alignment data and imported it into Microsoft Word.
- Using the find and replace tool in Microsoft Word, I added commas after every nucleotide and dash (which signified a deletion) to delimit the data.
- The delimited data was then transferred to Microsoft Excel.
The data was then analyzed in Microsoft Excel in a variety of steps.
- Each nucleotide base was color-coded for easy identification.
- Each subject was color coded based on their progressor group.
- I then found the "mode" of each column/base pair location using this website in order to find the consensus for each column.
- I calculated the ratio of # consensus:total number of clones for each column to get an idea of the hotspots.
- Then I calculated the percentage of nucleotide for each base pair location using the COUNTIF function.
- Conditional formatting rules were then used to color code the percentages with the 100% consensus base pairs marked in red.
- The previous two steps were repeated using only the progressor groups in each base pair location.
- Hotspots were found using a formula rule that analyzed the nucleotide percentages; if all the nucleotides had less than 80% of total, meaning there was no consensus, they were marked in purple on the base pair location number.
We found that certain base pair locations had preferences for certain nucleotides.
- I worked with Carolyn as my partner for the project by helping each other analyze data and create the presentation.
- I worked with Maya in class by helping each other with small tasks in Excel.
- I emailed Dr. Dahlquist for guidance in our analysis.
- I used and modified the Week 6 Protocol.
- Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
- OpenWetWare. (2020). BIOL368/S20:Week 6. Retrieved February 26, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_6
- Markham, R.B., Wang, W.C., Weisstein, A.E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., & Yu, X.F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 95, 12568-12573. doi: 10.1073/pnas.95.21.12568 (PubMed ID: 98445411)
- How to find the mode for text value from a list/column in Excel? ExtendOffice. Retrieved February 26, 2020, from https://www.extendoffice.com/documents/excel/3397-excel-find-mode-for-text.html