Matthew R Allegretti Week 4: Difference between revisions

Revision as of 16:11, 20 September 2016

Activity 2 Part 1 and 2 from Exploring HIV evolution: An opportunity for research.

Sketch your distance tree on paper so that you can make notes on it.
Do the clones from each subject cluster together?
Do some subjects' clones show more diversity than others?
Do some of the subjects cluster together?
Write a brief description of your tree and how you interpret the clustering pattern with respect to the similarities and potential evolutionary relationships between subjects' HIV sequences.
Copy and paste your tree from the Biology Workbench to share.

What is your question?
Make a prediction (hypothesis) about the answer to your question before you begin your analysis.
Which subjects, visits, and clones will you use to answer your question?
- You should choose a combination of subjects, visits, and clones that will add up to approximately 50 sequences. You will need about that many sequences to answer a reasonably complex question. However, you cannot use more because the multiple sequence alignment tool cannot handle more than that many sequences.
- Justify why you chose the subjects, visits, and clones you did.

Isai Lopez
While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
My partner and I agreed on our research topic.

Week 3 Instructions
Donovan, S., & Weisstein, A. E. (2003). Exploring HIV evolution: An opportunity for research. Stanley (Eds.), Microbes Count, 137-148.
Biology Workbench
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, 95(21), 12568-12573. Retrieved from http://bioquest.org/bedrock/problem_spaces/hiv/Markham_1998.pdf

@@ Line 28: / Line 28: @@
 ===Conclusion===
+==Research Project==
+# '''What is your question?'''
+# '''Make a prediction (hypothesis) about the answer to your question before you begin your analysis.'''
+# '''Which subjects, visits, and clones will you use to answer your question?'''
+#* You should choose a combination of subjects, visits, and clones that will add up to approximately 50 sequences.  You will need about that many sequences to answer a reasonably complex question.  However, you cannot use more because the multiple sequence alignment tool cannot handle more than that many sequences.
+#* '''Justify why you chose the subjects, visits, and clones you did.'''
 ==Acknowledgments==