Salomon Garcia: Week 9

Formulating our question for the next project and this is what we as a group came up with:

Sequence Alignment

• For this experiment we will be using the Markham et al Paper and we will also be using the Stanfield et al paper. These are the two links for them
  • Stanfield Article
  • 1. Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A, Margolick J, Vlahov D, Quinn T, Farzadegan H, and Yu XF. Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12568-73. DOI:10.1073/pnas.95.21.12568 |

• The sequence alignment was done for each of the Subjects in this case it was for subject 12 and subject 13, sequence alignment was done and this is what was shown for both of the subjects. The sequence alignment was done by using Biology WorkBench. These are the images that are seen:

Sequence Alignment for Subject 12

Sequence Alignment for Subject 13

Matricies

• Once the sequence alignment was done then a ClustalDist Matrix was ran in order to get the max for each of the clones and there particular visits and the matrix for both of the subjects is shown below.

Matrix for Subject 12

• min difference for subject 12= 1.045
• max difference for subject 12= 7.03

Matrix for Subject 13

• min difference for subject 13= 1.045
• max difference for subject 13= 7.03

• After this matrices were done the next thing that was done was look at each subject and look at two visits at a time for example visits 3 and 4 and then 4 clones were gathered for these visits

Box Shade of Protein Sequences

• For this portion of the project we sequences and we got a box shaded representation of our clones of Subject 12 and Subject 13 and this is what was seen:

Box Shading for Clones of Subject 12 and Subject 13

Rooted and Unrooted Trees

• Also from the sequence alignment of the 4 clones for each of the visits we get the rooted and unrooted trees and this is what it looks like.

Rooted Tree

Unrooted Tree

• For this experiment we decided on our article this is a Link to it:http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=78166
  • This is a the entire article in pdf file: Article by Lei Chen
  • This is the link to the Presentation on HIV Structure:PowerPoint Presentation Week 10

BIOL 398-01: Bioinformatics Lab

• Lab Journal

Salomon Garcia: Week 2	Salomon Garcia: Week 6	Salomon Garcia: Week 11
Salomon Garcia: Week 3	Salomon Garcia: Week 7	Salomon Garcia: Week 12
Salomon Garcia: Week 4	Salomon Garcia: Week 8	Salomon Garcia: Week 13
Salomon Garcia: Week 5	Salomon Garcia: Week 9	Salomon Garcia: Week 14

• 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
12. BIOL398-01/S10:Class Journal Week 14

• 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
12. BIOL398-01/S10:Week 14

Links

• Salomon Garcia Valencia
• Bioinformatics Lab Home