Mia Huddleston Week 4
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Electronic Lab Notebook
Purpose
Methods and Results
- I first want to upload “visit_1_S1_S9.txt” and “visit_1_S10_S15.txt” files into the nucleic acid tool set on my biology workbench
- I do this by logging into my Workbench, clicking on "nucleic tools," then downloading each file to the workbench
- I then generated a multiple sequence alignment and distance tree for 12 of these sequences
- I chose 3 clones from 4 subjects:
- Subjects: 15, 14, 10, and 8
- I chose 3 clones from 4 subjects:
- Looking at the tree shown above, the clones look like they tend to cluster together for each subject. However, subject 15's clones do not cluster as much as the others
- There is generally less diversity between each subject's clones compared to other subjects, again with the exception of subject 15 which shows much more genetic diversity than any of the others
- This can be seen through the length of the lines separating the clones
- Subjects 15, 14, and 10 are much more clustered together compared to subject 8
- This shows that subjects 15, 14, and 10 are much more genetically related than they are to subject 8. Because subject 10's clones are extremely close this means that there is very little genetic diversity between the clones where as the clones of subject 15 are much farther apart and therefore more diverse. Subject 14's clones are also very similarly related.
Data and Files
FASTA HIV downloaded sequences
Conclusion
Defining Our Research Project
References
- Websites used:
- NCBI website http://www.ncbi.nlm.nih.gov
- article link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC22871/
- Markham, R. B., Wang, W.-C., Weisstein, A. E., Wang, Z., Munoz, A., Templeton, A., … Yu, X.-F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proceedings of the National Academy of Sciences of the United States of America, 95(21), 12568–12573.
- article link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC22871/
- Biology Workbench website http://workbench.sdsc.edu
- NCBI website http://www.ncbi.nlm.nih.gov
Acknowledgments
This work was done with help from my homework partner, in class and with the help of our professor; Dr. Dahlquist. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
Useful links
User Page: Mia Huddleston
Bioinfomatics Lab: Fall 2016
Class Page: Bioinfomatics Laboratory, Fall 2016
