BIOL368/F14:Nicole Anguiano Week 5: Difference between revisions

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===Methods and Results===
===Methods and Results===
*First, I compiled the sequences of each of the clones that I'd specified [[BIOL368/F14:Nicole_Anguiano_Week_4 | last week]] (also listed above) from the [http://bioquest.org/bedrock/problem_spaces/hiv/nucleotide_sequences.php bioquest web site]. I went to the [http://workbench.sdsc.edu/ Biology workbench] and created a new session, called "Research". In this session, I uploaded the file I just created with all of the sequences.  
*First, I compiled the sequences of each of the clones that I'd specified [[BIOL368/F14:Nicole_Anguiano_Week_4 | last week]] (also listed above) from the [http://bioquest.org/bedrock/problem_spaces/hiv/nucleotide_sequences.php bioquest web site]. I went to the [http://workbench.sdsc.edu/ Biology workbench] and created a new session, called "Research". In this session, I uploaded the file I just created with all of the sequences.  
=====Visit 1=====
*I began by running a CLUSTALW on each of the first visit clones. I ran one on the rapid progressors, then the moderate progressors, then the nonprogressors, importing the alignments each time so that further analysis could be performed on each alignment through CLUSTALDIST.
*I began by running a CLUSTALW on each of the first visit clones. I ran one on the rapid progressors, then the moderate progressors, then the nonprogressors, importing the alignments each time so that further analysis could be performed on each alignment through CLUSTALDIST.
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[[Image:NP_V1_T.png|thumb|none|upright=2|alt=Nonprogressor Visit 1 Tree|<b>Figure 6</b>:The tree for subjects 2, 11, and 12 (the nonprogressors), generated by CLUSTALW.]]
[[Image:NP_V1_T.png|thumb|none|upright=2|alt=Nonprogressor Visit 1 Tree|<b>Figure 6</b>:The tree for subjects 2, 11, and 12 (the nonprogressors), generated by CLUSTALW.]]
<!--*Details on what is being seen in nons here...-->
<!--*Details on what is being seen in nons here...-->
*After running the CLUSTALW, I ran a CLUSTALDIST on each group to find the clustal distance matrix, and calculate the theta, min difference, and max difference (Table 1).  
*After running the CLUSTALW, I ran a CLUSTALDIST on each group to find the clustal distance matrix, and calculate the theta, min difference, and max difference (Table 1).  
[[Image:RP_V1_CDM.png|thumb|none|500px|alt=Rapid progressor visit 1 clustal distance matrix|<b>Figure 7</b>: The clustal distance matrix for subjects 3, 11, and 15 (the rapid progressors), generated by CLUSTALDIST. The min and max difference in Table 1 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 291.]]
[[Image:RP_V1_CDM.png|thumb|none|500px|alt=Rapid progressor visit 1 clustal distance matrix|<b>Figure 7</b>: The clustal distance matrix for subjects 3, 11, and 15 (the rapid progressors), generated by CLUSTALDIST. The min and max difference in Table 1 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 291.]]
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| Moderate and Nonprogressor || 21 || 48
| Moderate and Nonprogressor || 21 || 48
|-
|-
| All || - ||  
| All || 21 || 52
|}
|}
=====Mid-Visit=====
*I moved from the first visit clones to the mid-visit clones, and ran a CLUSTALW on each of the mid-visit clones. I ran one on the rapid progressors, then the moderate progressors, then the nonprogressors, importing the alignments each time so that further analysis could be performed on each alignment through CLUSTALDIST.
[[Image:RP_MV_SA.png|thumb|none|upright=3|alt=Rapid Progressor Mid-visit Sequence Alignment|<b>Figure 21</b>: The sequence alignment for subjects 3, 11, and 15 (the rapid progressors), generated by CLUSTALW. The S value in Table 3 was calculated by counting how many places there was a difference between the sequences.]]
[[Image:RP_MV_T.png|thumb|none|upright=2|alt=Rapid Progressor Mid-visit Tree |<b>Figure 22</b>2: The tree for subjects 3, 11, and 15 (the rapid progressors), generated by CLUSTALW.]]
<!--*Details on what is being seen in rapids here...-->
[[Image:MP_MV_SA.png|thumb|none|upright=3|alt=Moderate Progressor Mid-visit Sequence Alignment|<b>Figure 23</b>: The sequence alignment for subjects 6, 8, 14 (the moderate progressors), generated by CLUSTALW. The S value in Table 3 was calculated by counting how many places there was a difference between the sequences.]]
[[Image:MP_MV_T.png|thumb|none|upright=2|alt=Moderate Progressor Mid-visit Tree |<b>Figure 24</b>2: The tree for subjects 6, 8, 14 (the moderate progressors), generated by CLUSTALW.]]
<!--*Details on what is being seen in moderates here...-->
[[Image:NP_MV_SA.png|thumb|none|upright=3|alt=Nonprogressor Mid-visit Sequence Alignment|<b>Figure 25</b>: The sequence alignment for subjects 2, 12, 13 (the nonprogressors), generated by CLUSTALW. The S value in Table 3 was calculated by counting how many places there was a difference between the sequences.]]
[[Image:NP_MV_T.png|thumb|none|upright=2|alt=Nonprogressor Mid-visit Tree |<b>Figure 26</b>2: The tree for subjects 2, 12, 13 (the nonprogressors), generated by CLUSTALW.]]
<!--*Details on what is being seen in moderates here...-->
*After running the CLUSTALW, I ran a CLUSTALDIST on each group to find the clustal distance matrix, and calculate the theta, min difference, and max difference (Table 3).
[[Image:RP_MV_CDM.png|thumb|none|500px|alt=Rapid progressor mid-visit clustal distance matrix|<b>Figure 27</b>: The clustal distance matrix for subjects 3, 11, and 15 (the rapid progressors), generated by CLUSTALDIST. The min and max difference in Table 3 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 291.]]
<!--*Details on what is being seen in rapids here...-->
[[Image:MP_MV_CDM.png|thumb|none|500px|alt=Moderate progressor mid-visit clustal distance matrix|<b>Figure 28</b>: The clustal distance matrix for subjects 6, 8, and 14 (the moderate progressors), generated by CLUSTALDIST. The min and max difference in Table 3 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 288.]]
<!--*Details on what is being seen in moderates here...-->
[[Image:NP_MV_CDM.png|thumb|none|500px|alt=Nonprogressor mid-visit clustal distance matrix|<b>Figure 29</b>: The clustal distance matrix for subjects 2, 12, and 13 (the nonprogressors), generated by CLUSTALDIST. The min and max difference in Table 3 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 285.]]
<!--*Details on what is being seen in nons here...-->
{|border="1"
|-
!Group !! S !! θ !! Min Difference !! Max Difference
|-
| Rapid Progressors || 83 || - || 41 || 52
|-
| Moderate Progressors || 50 || - || 12 || 32
|-
| Nonprogressors || 58 || - || 22 || 45
|}


*I repeated all of the above steps with the clones taken from the 2-year visit instead of the first visit. After that, I ran a CLUSTALW and CLUSTALDIST on all of the clones over all of the visits.
*I repeated all of the above steps with the clones taken from the 2-year visit instead of the first visit. After that, I ran a CLUSTALW and CLUSTALDIST on all of the clones over all of the visits.

Revision as of 10:55, 30 September 2014

Electronic Lab Notebook

Answering the question: Do clones from a particular subject's group (rapidly progressing, moderately progressing, and nonprogressing), share any genetic similarity with one another? Are clones from subjects in the same group the most similar, or are they as dissimilar as clones from other groups? Does the amount of variation and similarity, if any, change from the time of the first visit to a visit after about 2 years of infection with the virus?

Below are the clones chosen and the subjects/visits they are from:

Progressor Group Subject Visit # Clones Visit # Clones
Rapid 3 1 1, 2, 3 3 2, 7, 9
Rapid 11 1 3, 5, 7 3 3, 6, 9
Rapid 15 1 3, 6, 12 4 1, 3, 4
Moderate 6 1 1, 2, 3 5 2, 4, 8
Moderate 8 1 1, 3, 5 4 4, 5, 6
Moderate 14 1 2, 3, 6 5 1, 6, 7
Nonprogressor 2 1 3, 4, 5 3 5, 6, 7
Nonprogressor 12 1 1, 2, 3 4 2, 5, 10
Nonprogressor 13 1 1, 3, 4 3 1, 2, 4


Methods and Results

  • First, I compiled the sequences of each of the clones that I'd specified last week (also listed above) from the bioquest web site. I went to the Biology workbench and created a new session, called "Research". In this session, I uploaded the file I just created with all of the sequences.
Visit 1
  • I began by running a CLUSTALW on each of the first visit clones. I ran one on the rapid progressors, then the moderate progressors, then the nonprogressors, importing the alignments each time so that further analysis could be performed on each alignment through CLUSTALDIST.
Rapid Progressor Visit 1 Sequence Alignment
Figure 1: The sequence alignment for subjects 3, 11, and 15 (the rapid progressors), generated by CLUSTALW. The S value in Table 1 was calculated by counting how many places there was a difference between the sequences.
Rapid Progressor Visit 1 Tree
Figure 22: The tree for subjects 3, 11, and 15 (the rapid progressors), generated by CLUSTALW.
Moderate Progressor Visit 1 Sequence Alignment
Figure 3: The sequence alignment for subjects 6, 8, and 14 (the moderate progressors), generated by CLUSTALW. The S value in Table 1 was calculated by counting how many places there was a difference between the sequences.
Moderate Progressor Visit 1 Tree
Figure 4: The tree for subjects 6, 8, and 14 (the moderate progressors), generated by CLUSTALW.
Nonprogressor Visit 1 Sequence Alignment
Figure 5: The sequence alignment for subjects 2, 11, and 12 (the nonprogressors), generated by CLUSTALW. The S value in Table 1 was calculated by counting how many places there was a difference between the sequences.
Nonprogressor Visit 1 Tree
Figure 6:The tree for subjects 2, 11, and 12 (the nonprogressors), generated by CLUSTALW.
  • After running the CLUSTALW, I ran a CLUSTALDIST on each group to find the clustal distance matrix, and calculate the theta, min difference, and max difference (Table 1).
Rapid progressor visit 1 clustal distance matrix
Figure 7: The clustal distance matrix for subjects 3, 11, and 15 (the rapid progressors), generated by CLUSTALDIST. The min and max difference in Table 1 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 291.
Moderate progressor visit 1 clustal distance matrix
Figure 8: The clustal distance matrix for subjects 6, 8, and 14 (the moderate progressors), generated by CLUSTALDIST. The min and max difference in Table 1 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 288.
Nonprogressor visit 1 clustal distance matrix
Figure 9: The clustal distance matrix for subjects 2, 12, and 13 (the nonprogressors), generated by CLUSTALDIST. The min and max difference in Table 1 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 285.
Group S θ Min Difference Max Difference
Rapid Progressors 83 - 39 52
Moderate Progressors 49 - 14 32
Nonprogressors 55 - 22 44
  • Table 1
  • After comparing each group with itself, I then compared across groups. I ran a CLUSTALW and CLUSTALDIST on the first visit clones from the three rapid progressors and the three moderate progressors, then the three rapid progressors and the three nonprogressors, then the three moderate progressors and the three nonprogressors. After the comparison, I ran a CLUSTALW and CLUSTALDIST on all of the visit 1 clones.
Rapid Progressor and Moderate Progressor Visit 1 Tree
Figure 11:The tree for the rapid and moderate progressors, generated by CLUSTALW.
Rapid Progressor and Moderate Progressor Visit 1 Clustal Distance Matrix
Figure 12:The clustal distance matrix for the rapid and moderate progressors, generated by CLUSTALDIST. The min and max difference in Table 2 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 291.
Rapid Progressor and Nonprogressor Visit 1 Tree
Figure 14:The tree for the rapid and nonprogressors, generated by CLUSTALW.
Rapid Progressor and Nonprogressor Visit 1 Clustal Distance Matrix
Figure 15:The clustal distance matrix for the rapid and nonprogressors, generated by CLUSTALDIST. The min and max difference in Table 2 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 291.
Moderate Progressor and Nonprogressor Visit 1 Tree
Figure 17:The tree for the moderate and nonprogressors, generated by CLUSTALW.
Moderate Progressor and Nonprogressor Visit 1 Clustal Distance Matrix
Figure 18:The clustal distance matrix for the moderate and nonprogressors, generated by CLUSTALDIST. The min and max difference in Table 2 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 288.
Visit 1 Tree
Figure 19:The tree for the all three progressor groups for visit 1, generated by CLUSTALW.
Visit 1 Clustal Distance Matrix
Figure 20:The clustal distance matrix for all three progressor groups for visit 1, generated by CLUSTALDIST. The min and max difference in Table 2 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 291.
Groups Being Compared Min Difference Max Difference
Rapid and Moderate 19 56
Rapid and Nonprogressor 24 54
Moderate and Nonprogressor 21 48
All 21 52
Mid-Visit
  • I moved from the first visit clones to the mid-visit clones, and ran a CLUSTALW on each of the mid-visit clones. I ran one on the rapid progressors, then the moderate progressors, then the nonprogressors, importing the alignments each time so that further analysis could be performed on each alignment through CLUSTALDIST.
Rapid Progressor Mid-visit Sequence Alignment
Figure 21: The sequence alignment for subjects 3, 11, and 15 (the rapid progressors), generated by CLUSTALW. The S value in Table 3 was calculated by counting how many places there was a difference between the sequences.
Rapid Progressor Mid-visit Tree
Figure 222: The tree for subjects 3, 11, and 15 (the rapid progressors), generated by CLUSTALW.
Moderate Progressor Mid-visit Sequence Alignment
Figure 23: The sequence alignment for subjects 6, 8, 14 (the moderate progressors), generated by CLUSTALW. The S value in Table 3 was calculated by counting how many places there was a difference between the sequences.
Moderate Progressor Mid-visit Tree
Figure 242: The tree for subjects 6, 8, 14 (the moderate progressors), generated by CLUSTALW.
Nonprogressor Mid-visit Sequence Alignment
Figure 25: The sequence alignment for subjects 2, 12, 13 (the nonprogressors), generated by CLUSTALW. The S value in Table 3 was calculated by counting how many places there was a difference between the sequences.
Nonprogressor Mid-visit Tree
Figure 262: The tree for subjects 2, 12, 13 (the nonprogressors), generated by CLUSTALW.
  • After running the CLUSTALW, I ran a CLUSTALDIST on each group to find the clustal distance matrix, and calculate the theta, min difference, and max difference (Table 3).
Rapid progressor mid-visit clustal distance matrix
Figure 27: The clustal distance matrix for subjects 3, 11, and 15 (the rapid progressors), generated by CLUSTALDIST. The min and max difference in Table 3 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 291.
Moderate progressor mid-visit clustal distance matrix
Figure 28: The clustal distance matrix for subjects 6, 8, and 14 (the moderate progressors), generated by CLUSTALDIST. The min and max difference in Table 3 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 288.
Nonprogressor mid-visit clustal distance matrix
Figure 29: The clustal distance matrix for subjects 2, 12, and 13 (the nonprogressors), generated by CLUSTALDIST. The min and max difference in Table 3 was calculated by comparing across subjects and seeing what the highest and lowest values were, then multiplying by 285.
Group S θ Min Difference Max Difference
Rapid Progressors 83 - 41 52
Moderate Progressors 50 - 12 32
Nonprogressors 58 - 22 45


  • I repeated all of the above steps with the clones taken from the 2-year visit instead of the first visit. After that, I ran a CLUSTALW and CLUSTALDIST on all of the clones over all of the visits.

Conclusions

Other notes

Links

Nicole Anguiano
BIOL 368, Fall 2014

Assignment Links
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