Salomon Garcia: Week 9

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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
  • 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 12
Sequence Alignment for Subject 13
Sequence Alignment for Subject 13


  • 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
Matrix for Subject 12
  • min difference for subject 12= 1.045
  • max difference for subject 12= 7.03
Matrix for Subject 13
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
Rooted Tree
Unrooted Tree
Unrooted Tree

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


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