Janelle N. Ruiz Assignment 4

Activity 1/Part 2: GenBank

• Question 1: The accession number of the sequence I chose was AF016760.

• Question 2: This HIV-1 sequence came from subject 1. The first part of the record, labeled “Definition” is the section of the record where I found this information.

• Task 3: Download several (4-6) sequences in FASTA format to your local hard drive:

Activity 1/Part 3: Introduction to the Biology Workbench

• Task 1: Select all of your sequences (seen above) using the appropriate command and run a multiple sequence alignment using Clustal W:

Activity 2/Part 1: Looking at clustering across subjects

Analysis of the 97 sequences from the 15 subjects' first visits

• Task 1: Generate a multiple sequence analysis and distance tree for 12 of these sequences (3 clones from each of 4 subjects)

• Question 1: The clones from each subject do tend to cluster together, as shown by the tree above.

• Question 2: Clones show more diversity than subject 4 clones. Subject 1 and 2 clones show similar diversity to one another and to subject 3 clones.

• Question 3: Subject 1 and 2 clones cluster together indicating that these clones have a high genetic similarity while the clones from subject 3 and 4 have a high genetic difference from one another and from subject 1 and 2 as a group.

• Question 4: Subject 1 and 2 clones are similar genetically indicating that thye may have a close evolutionary relationship, potentially arising from the same virus. Subject 3 clones have high genetic distance from subject 4 and 1 and 2. Subject 4 clones are more closely realted to subject 1 and 2 clones than subject 3 clones, indicating that subject 4 clones may have diverged evolutionarily more recently from 1 and 2 than Subject 3 clones.

Activity 2/Part 2: Quantifying diversity within and between subjects

• Task 1: Find S and Theta for 3 Subjects

• Example data, Subject 1

• Task 2: Find Min and Max difference ACROSS subjects (1, 2, & 3)

• Example data, Subject 1 & 2

Janelle N. Ruiz

Class Links

BIOL 398.01/Spring 2010

Journal Assignments

Janelle N. Ruiz Assignment 2	Janelle N. Ruiz Assignment 5	Janelle N. Ruiz Assignment 8	Janelle N. Ruiz Assignment 12	Janelle N. Ruiz Assignment 14
Janelle N. Ruiz Assignment 3	Janelle N. Ruiz Assignment 6	Janelle N. Ruiz Assignment 9	Janelle N. Ruiz Assignment 13	Janelle N. Ruiz Assignment 15
Janelle N. Ruiz Assignment 4	Janelle N. Ruiz Assignment 7	Janelle N. Ruiz Assignment 11

• Shared Journal

1. BIOL398-01/S10:Class Journal Week 2
2. BIOL398-01/S10:Class Journal Week 3
3. BIOL398-01/S10:Class Journal Week 4
4. BIOL398-01/S10:Class Journal Week 5
5. BIOL398-01/S10:Class Journal Week 6
6. BIOL398-01/S10:Class Journal Week 7
7. BIOL398-01/S10:Class Journal Week 8
8. BIOL398-01/S10:Class Journal Week 9
9. BIOL398-01/S10:Class Journal Week 11
10. BIOL398-01/S10:Class Journal Week 12
11. BIOL398-01/S10:Class Journal Week 13

• Assignments

1. BIOL398-01/S10:Week 2
2. BIOL398-01/S10:Week 3
3. BIOL398-01/S10:Week 4
4. BIOL398-01/S10:Week 5
5. BIOL398-01/S10:Week 6
6. BIOL398-01/S10:Week 7
7. BIOL398-01/S10:Week 8
8. BIOL398-01/S10:Week 9
9. BIOL398-01/S10:Week 11
10. BIOL398-01/S10:Week 12
11. BIOL398-01/S10:Week 13