AVM BIOL368 Week 4

Purpose

• To continue with our class research and journal projects for the Markham et al. paper
  • Continue to learn about sequencing and the similarities and differences

Part 1

• Upload the “visit_1_S1_S9.txt” and “visit_1_S10_S15.txt” files from the BIOL368/F16 Week 4 page into the Biology Workbench
• Generate a multiple sequence alignment using ClustlW
  • Choose 3 clones form 4 different subjects (as shown in table below)

• • Photo of tree shown below

• • Notice that the clones from each subject group together
  • In subject 3, mutation 3 is more diverse than mutations 1 and 2, which are more closely related
  • Also note that some of the subjects cluster together (clones from subjects 1 and 2)
    • Subject 4 clones may be more related to subjects 1 and 2
    • This tree shows that Subject 1 and 2 have very closely related viruses, and within this virus, mutations 1 and 2 of subject 2 are most closely related to mutation 3 of subject 1. All of the mutations of subject 4's virus are most closely related to each other and the mutations of subject 3 are most closely related to each other.

Part 2

• Select a sequence from last weeks assignment and align all of the clones
• Calculate S from the alignment
  • S is the number of positions where there is at least one nucleotide difference across the clones
• Save the alignment for later use
• Run an analysis for two more subjects
  • Sequence differences for each subject shown at right

Subject 6

Subject 8

Subject 14

• • (Math Is Fun was used to calculate theta)
• Within the Clustdist tool generate a distance matrix for one of your alignments
• Choose the highest and lowest pairwise scores and find the % difference
• Calculate theta for each subject
  • Repeat these steps for each subject
  • Table below shows results from these analysis

• Create a new alignment with all the sequences from 2 different subjects
• Use Clustdist to create a pairwise distance matrix
• Find all the min and max differences
  • Results shown in table below

Research Project

1. What is your question?
   • If HIV-1 virus evolution patterns are based on virus copy number rather than CD4 T-cell decline, how would this change the subjects classification as non-progressors, moderate progressors, and rapid progress ors? Is virus copy number correlated with diversity and divergence?
2. Make a prediction (hypothesis) about the answer to your question before you begin your analysis.
   • There would be a shift in the subjects being grouped as moderate and rapid progressors. There is an overlap in virus number copies in Table 1 for subjects in both of these groups.
3. Which subjects, visits, and clones will you use to answer your question?
   • We could look at subjects 1, 3, 6 and 7 as they have very similar virus number copies. We could also choose subjects 12 and 13 to compare to those which have significantly lower virus number copies.
   • 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.

References

User: Avery_Vernon-Moore

Weekly Assignments:

Assignment 1
Assignment 2
Assignment 3
Assignment 4
Assignment 5
Assignment 6
Assignment 7
Assignment 8
Assignment 9
Assignment 10
Assignment 11
Assignment 12
Assignment 14
Assignment 15

Individual Journals:

"Week 1: Create Wiki Page" 
Individual Journal 2
Individual Journal 3
Individual Journal 4
Individual Journal 5
Individual Journal 6
Individual Journal 7
Individual Journal 8
Individual Journal 9
Individual Journal 10
Individual Journal 11
Individual Journal 12
No Week 13 Assignment
Individual Journal 14
Individual Journal 15

Shared Journals:

Class Journal 1
Class Journal 2
Class Journal 3
Class Journal 4
Class Journal 5
Class Journal 6
Class Journal 7
Class Journal 8
Class Journal 9
Class Journal 10
Class Journal 11
Class Journal 12
Class Journal 14
Class Journal 15