Janelle N. Ruiz Assignment 4

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Contents

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.

GenBank Record 1

GenBank Record 1

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

Image:BioScreenShot3.JPG

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:

Image:BioScreenShot7 LABELS.JPG

Image:BioScreenShot4.JPG

Image:BioScreenShot5.JPG

Image:BioScreenShot6.JPG

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)

Table 2

Image:Part1sequenceshot.JPG Image:Part1sequenceshot1.JPG

Image:Part1 Tree.JPG

  • 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

Table 3

  • Example data, Subject 1

Image:ClustalDistS1.JPG

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

Table 4

  • Example data, Subject 1 & 2

Image:ClustalDist1 2.JPG

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
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