BIOL368/F14:Isabel Gonzaga Week 5: Difference between revisions

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BIOL368/F14:Isabel Gonzaga Week 5 (view source)

Revision as of 17:47, 30 September 2014

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In both trees, Red represents subjects diagnosed with AIDs, Yellow represents subjects trending towards AIDS and Blue represents subjects with no trend of progression towards the disease.
In both trees, Red represents subjects diagnosed with AIDs, Yellow represents subjects trending towards AIDS and Blue represents subjects with no trend of progression towards the disease.
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 HIV-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:AIDS MSA F.png|thumb|left|300px|<b>Figure 4.</b> ClustalW alignment for all HIV-diagnosed 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 Diagnosed 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:Progressingclustadistv2.png|thumb|left|300px|<b>Figure 7.</b> Clustadist analysis for all AIDS-progressing sequences at the time of their initial visits. Minimum and Maximum base pair values were calculated using this matrix]]
[[Image:Notrendclustadistv1.png|thumb|left|300px|<b>Figure 8.</b> Clustadist analysis for all Non-trending sequences at the time of their initial visits. Minimum and Maximum base pair values were calculated using this matrix]]
[[Image:DiagnosedvsProgressingClustadistV1.png|thumb|left|300px|<b>Figure 9.</b> Clustadist analysis comparing AIDS diagnosed and AIDS-Progressing sequences at the time of their initial visits. Minimum and Maximum base pair values were calculated using this matrix]]
[[Image:AIDSvsNoTrendClustadistV1.png|thumb|left|300px|<b>Figure 10.</b> Clustadist analysis comparing AIDS diagnosed and Non-Trending sequences at the time of their initial visits. Minimum and Maximum base pair differences were calculated using this matrix]]
[[Image:ProgressingVsNoTrendClustadistV1.png |thumb|left|300px|<b>Figure 11.</b> Clustadist analysis comparing AIDS-Progressing and Non-Trending sequences at the time of their initial visits. Minimum and Maximum base pair differences were calculated using this matrix]]
[[Image:AIDS MSA F.png|thumb|left|300px|<b>Figure 12.</b> ClustalW alignment for all AIDS-diagnosed 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 Diagnosed 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:AIDSClustadistVF.png|thumb|left|300px|<b>Figure 15.</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:ProgressingClustadistvF.png|thumb|left|300px|<b>Figure 16.</b> Clustadist analysis for all AIDS-progressing sequences at the time of their initial 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 initial 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 initial visits. Minimum and Maximum base pair values were calculated using this matrix]]
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<b>Initial Visit</b><Br>
<b>Initial Visit</b><Br>
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