Chris Rhodes Week 5: Difference between revisions

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[[Image:CHR_Image3_20110928.gif | Subject 3 Rooted Tree]]
[[Image:CHR_Image3_20110928.gif | Subject 3 Rooted Tree]]


Based on both the rooted and unrooted trees you can see that subject 3 had very high diversity and divergence. The rooted tree shows a large vertical distance between its two ends and a large amount of branching with no branch being prominent. The clones seem to cluster together based on their visit number to create the various branches and show little similarity with clones outside of their own visit.The only exceptions to this pattern are some of the clones of visit 4 who share greater similarities to visit 1 or 3 clones rather than with other visit 4 clones. However, this overall pattern is indicative of an immune response in which there is high selection happening against no change in the amino acid sequence which results in large divergence every visit.
Based on both the rooted and unrooted trees you can see that subject 3 had very high diversity and divergence. The rooted tree shows a large vertical distance between its two ends and a large amount of branching with no branch being prominent. The clones seem to cluster together based on their visit number to create the various branches and show little similarity with clones outside of their own visit.The only exceptions to this pattern are some of the clones of visit 4 who share greater similarities to visit 1 or 3 clones rather than with other visit 4 clones. However, this overall pattern is indicative of an immune response in which there is high selection happening against no change in the amino acid sequence which results in large divergence every visit. This hypothesis however, differs with the dS/dN value of 1 for Subject 3 which, according to the paper, would indicate that there is no selection either for or against change in the amino acid sequence.
*Subject 7
*Subject 7
'''Unrooted Tree'''
'''Unrooted Tree'''

Revision as of 13:08, 3 October 2011

Methods

  • To create ClustalW alignments and phylogenetic trees for the chosen subjects(3,7,8,11,12, and 13) each subject's sequence datawas uploaded onto Workbench each as a separate session.

Workbench Sessions

  • For each subject's clones a ClustalW alignment was run using default parameters to generate both the rooted and unrooted phylogenetic trees.
  • Subject 3

Unrooted Tree Subject 3 Unrooted Tree

Rooted Tree Subject 3 Rooted Tree

Based on both the rooted and unrooted trees you can see that subject 3 had very high diversity and divergence. The rooted tree shows a large vertical distance between its two ends and a large amount of branching with no branch being prominent. The clones seem to cluster together based on their visit number to create the various branches and show little similarity with clones outside of their own visit.The only exceptions to this pattern are some of the clones of visit 4 who share greater similarities to visit 1 or 3 clones rather than with other visit 4 clones. However, this overall pattern is indicative of an immune response in which there is high selection happening against no change in the amino acid sequence which results in large divergence every visit. This hypothesis however, differs with the dS/dN value of 1 for Subject 3 which, according to the paper, would indicate that there is no selection either for or against change in the amino acid sequence.

  • Subject 7

Unrooted Tree Subject 7 Unrooted Tree

Rooted Tree Subject 7 Rooted Tree

  • Subject 8

Unrooted Tree Subject 8 Unrooted Tree

Rooted Tree Subject 8 Rooted Tree

  • Subject 11

Unrooted Tree Subject 11 Unrooted Tree

Rooted Tree Subject 11 Rooted Tree

  • Subject 12

Unrooted Tree Subject 12 Unrooted Tree

Rooted Tree Subject 12 Rooted Tree

  • Subject 13

Unrooted Tree Subject 13 Unrooted Tree

Rooted Tree Subject 13 Rooted Tree

References

[1]

Links

  1. Chris Rhodes User Page
  2. Week 2 Journal
  3. Week 3 Journal
  4. Week 4 Journal
  5. Week 5 Journal
  6. Week 6 Journal
  7. Week 7 Journal
  8. Week 8 Journal
  9. Week 9 Journal
  10. Week 10 Journal
  11. Week 11 Journal
  12. Week 12 Journal
  13. Week 13 Journal
  14. Week 14 Journal
  15. Home Page
  16. Week 5 Assignment Page
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  23. Week 12 Assignment Page
  24. Week 13 Assignment Page
  25. Week 14 Assignment Page
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