Courtney L. Merriam Week 4
From OpenWetWare
Purpose
The purpose of this experiment was to
Methods and Results
Activity 2 Part 1:
- Upload the “visit_1_S1_S9.txt” and “visit_1_S10_S15.txt” files into the nucleic acid tool set of the Biology Workbench session created in the last exercise.
- Generate a multiple sequence alignment and distance tree for 12 of these sequences (3 clones from each of 4 subjects).
- Sketch the 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 the tree and how to 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 into a word processor and print it out to share with the class.
Activity 2 Part 2:
- Select all the clones from one subject and align them. From the alignment calculate S by counting the number of positions where there is at least one nucleotide difference across the collection of clones. Enter data into Table 3
- Import your alignment so that you can use it in a later section.
- Run the same analysis for a second and third subject and record your results in Table 3.
- Calculate θ for the three subjects chosen to work with and enter the results in the datable.
- Use the Clustdist tool in the alignment tool set to generate a distance matrix for an alignment saved.
- Select the highest and lowest pairwise scores and convert that percentage difference score into the raw number of differences by multiplying by the length of the sequence.
- Round to the nearest integer, record your results in Table 3 and repeat the analysis for the other 2 subjects.
- Create a new alignment with all of the sequences from 2 subjects.
- Use Clustdist to generate a pairwise distance matrix for the alignment across subjects and find the minimum and maximum differences between the subjects sequences. Remember, only at pairwise distances across subjects, not within one subject.
- Record data in Table 4 and repeat the analysis for the other pairs of subjects.
Data and Files
No files or data was used for this assignment.
Conclusion
What was your main finding for today's exercise? Did you fulfill the purpose? Why or why not?
Defining Your 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? Justify why you chose the subjects, visits, and clones you did.
Acknowledgments
I collaborated with Avery Vernon-Moore and [[User:]] in class on this assignment. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
References
[http://
Useful Links
Clas Page: Bioinformatics Laboratory
| Weekly Assignments | Individual Journal Assignments | Shared Journal Assignments |
|---|---|---|
|
|
|
