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BIOL368/F14:Isabel Gonzaga Week 5: Difference between revisions
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BIOL368/F14:Isabel Gonzaga Week 5 (view source)
Revision as of 16:21, 26 September 2014
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=Methods and Results= | =Methods and Results= | ||
Biology WorkBench was used to compare and analyze the dataset. A ClustalW was performed for all sequences from the first visit, and all sequences from the final visit. The following rootless trees were generated and color coded:<br> | *The following sequences was taken from the [http://bioquest.org/bedrock/problem_spaces/hiv/nucleotide_sequences.php BEDROCK HIV Problem Space Database], from the Markham et al. (1998) study. The sequence were compiled into a [[Media:All_Subjects.txt|single text document]] in FASTA format: | ||
**<b>AIDS</b> | |||
***Subject 3 | |||
****S3V1 (1-3), S3V6 (3,5,6 | |||
***Subject 10 | |||
****S10V1 (3,5,7), S10V6 (4,6,8) | |||
***Subject 15 | |||
****S15V1 (6,9,12), S15V4 (2,6,8) | |||
**<b>Progressing Towards AIDS</b> | |||
***Subject 8 | |||
****S8V1 (1,2,4), S8V7 (3,5,7) | |||
***Subject 9 | |||
****S9V1 (2-4), S9V8 (2,4,8) | |||
***Subject 14 | |||
****S14V1 (2,5,6), S14V9 (3,6,9) | |||
**<b>No Trend</b> | |||
***Subject 5 | |||
****S5V1 (2,4,6), S5V5 (1,3,4) | |||
***Subject 6 | |||
****S6V1 (1-3), S6V8(4,6,8) | |||
***Subject 13 | |||
****S13V1 (2-4), S13V5 (1,2,4) | |||
Biology WorkBench was used to compare and analyze the dataset. The sequence file was uploaded onto a new session for analysis. A ClustalW was performed for all sequences from the first visit, and all sequences from the final visit. The following rootless trees were generated and color coded:<br> | |||
[[Image:Unrooted_Tree_-_Visit_1cc.png]]<br> | [[Image:Unrooted_Tree_-_Visit_1cc.png]]<br> | ||
[[Image:Unrooted_Tree_-_Final_Visitcc.png]] | [[Image:Unrooted_Tree_-_Final_Visitcc.png]] | ||
<br><Br> | <br><Br> | ||
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. | ||
