296
edits
BIOL368/F14:Isabel Gonzaga Week 5: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
BIOL368/F14:Isabel Gonzaga Week 5 (view source)
Revision as of 18:07, 30 September 2014
, 30 September 2014finished adding tables and figures
(Added most figures) |
(finished adding tables and figures) |
||
| Line 26: | Line 26: | ||
ClustalW was performed for each group from Visit 1. Sequences were aligned and further analyzed using the ClustalDist analysis, where minimum and maximum base pair differences were calculated within each AIDs status group. Groupings were further analyzed in comparison to each other. ClustalW was performed for AIDS diagnosed and AIDS progressing subjects. The sequences were aligned and a Clustaldist was performed to calculate minimum and maximum differences between strains within the two groups. This was repeated for AIDS diagnosed and No Trend, as well as AIDS progressing and no trend. These processes were repeated for the Final Visit sequences. The findings and calculations are as follows: | ClustalW was performed for each group from Visit 1. Sequences were aligned and further analyzed using the ClustalDist analysis, where minimum and maximum base pair differences were calculated within each AIDs status group. Groupings were further analyzed in comparison to each other. ClustalW was performed for AIDS diagnosed and AIDS progressing subjects. The sequences were aligned and a Clustaldist was performed to calculate minimum and maximum differences between strains within the two groups. This was repeated for AIDS diagnosed and No Trend, as well as AIDS progressing and no trend. These processes were repeated for the Final Visit sequences. The findings and calculations are as follows: | ||
[[Image:AIDSV1alignment.jpg|thumb|left|300px|<b>Figure 3.</b> ClustalW alignment for all AIDS-diagnosed sequences at the time of the first visit. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the AIDS Diagnosed groups.]] | [[Image:AIDSV1alignment.jpg|thumb|left|300px|<b>Figure 3.</b> ClustalW alignment for all AIDS-diagnosed sequences at the time of the first visit. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the AIDS Diagnosed groups.]] | ||
[[Image:Progressingclustal1.png|thumb|left|300px|<b>Figure 4.</b> ClustalW alignment for all AIDS-progressing sequences at the time of the first visit. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the AIDS Progressing groups.]] | |||
[[Image:Notrendclustal1.png|thumb|left|300px|<b>Figure 5.</b> ClustalW alignment for all No-Trend sequences at the time of the first visit. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the Non-Trending groups.]] | |||
[[Image:Aids_clustadist_v1.png|thumb|left|300px|<b>Figure 6.</b> Clustadist analysis for all AIDS-diagnosed sequences at the time of their initial visits. Minimum and Maximum base pair values were calculated using this matrix]] | [[Image:Aids_clustadist_v1.png|thumb|left|300px|<b>Figure 6.</b> Clustadist analysis for all AIDS-diagnosed sequences at the time of their initial visits. Minimum and Maximum base pair values were calculated using this matrix]] | ||
| Line 39: | Line 39: | ||
[[Image:ClustalWProgressingVF.png|thumb|left|300px|<b>Figure 13.</b> ClustalW alignment for all AIDS-progressing sequences at the time of their final visits. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the AIDS Progressing groups.]] | [[Image:ClustalWProgressingVF.png|thumb|left|300px|<b>Figure 13.</b> ClustalW alignment for all AIDS-progressing sequences at the time of their final visits. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the AIDS Progressing groups.]] | ||
[[Image:ClustalWNoTrendVF.png|thumb|left|300px|<b>Figure 14.</b> ClustalW alignment for all Non-Trending sequences at the time of their final visits. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the Non-Trending groups.]] | [[Image:ClustalWNoTrendVF.png|thumb|left|300px|<b>Figure 14.</b> ClustalW alignment for all Non-Trending sequences at the time of their final visits. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the Non-Trending groups.]] | ||
[[Image:AIDSClustadistVF.png|thumb|left|300px|<b>Figure 15.</b> Clustadist analysis for all AIDS-diagnosed sequences at the time of their | [[Image:AIDSClustadistVF.png|thumb|left|300px|<b>Figure 15.</b> Clustadist analysis for all AIDS-diagnosed sequences at the time of their final visits. Minimum and Maximum base pair values were calculated using this matrix]] | ||
[[Image:ProgressingClustadistvF.png|thumb|left|300px|<b>Figure 16.</b> Clustadist analysis for all AIDS-progressing sequences at the time of their | [[Image:ProgressingClustadistvF.png|thumb|left|300px|<b>Figure 16.</b> Clustadist analysis for all AIDS-progressing sequences at the time of their final visits. Minimum and Maximum base pair values were calculated using this matrix]] | ||
[[Image:AIDSvsProgressingClustadistVF.png|thumb|left|300px|<b>Figure 18.</b> Clustadist analysis comparing AIDS diagnosed and AIDS-Progressing sequences at the time of their | [[Image:Nonclustadistvf.png|thumb|left|300px|<b>Figure 17.</b> Clustadist analysis for all Non-Trending sequences at the time of their final visits. Minimum and Maximum base pair values were calculated using this matrix]] | ||
[[Image:ProgressingVsNoTrendClustadistVF.png|thumb|left|300px|<b>Figure 20.</b> Clustadist analysis comparing AIDS Progressing and Non-Trending sequences at the time of their | [[Image:AIDSvsProgressingClustadistVF.png|thumb|left|300px|<b>Figure 18.</b> Clustadist analysis comparing AIDS diagnosed and AIDS-Progressing sequences at the time of their final visits. Minimum and Maximum base pair values were calculated using this matrix]] | ||
[[Image:Aidsvsnonclustadistvf.png|thumb|left|300px|<b>Figure 19.</b> Clustadist analysis comparing AIDS diagnosed and Non-Trending sequences at the time of their final visits. Minimum and Maximum base pair values were calculated using this matrix]] | |||
[[Image:ProgressingVsNoTrendClustadistVF.png|thumb|left|300px|<b>Figure 20.</b> Clustadist analysis comparing AIDS Progressing and Non-Trending sequences at the time of their final visits. Minimum and Maximum base pair values were calculated using this matrix]] | |||
<br><Br> | <br><Br> | ||
<b>Initial Visit</b><Br> | <b>Initial Visit</b><Br> | ||
