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:









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