BIOL368/F14:Isabel Gonzaga Week 5: Difference between revisions
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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. | ||
Revision as of 23:21, 26 September 2014
HIV Evolution Research Project - Introduction
- Question: Is there a relationship between the genetic identities in the viral strains present in Subjects with or progressing towards AIDS diagnosis, compared to subjects who are not?
- Hypothesis: I predict that in comparing and analyzing subjects of these three categories (diagnosed with AIDS, trending towards AIDS and no trend), higher diversity will be found in the AIDS diagnosed and in those trending towards AIDS. I also hypothesize that the 'no trend' group will maintain some genetic similarity across viruses.
Methods and Results
- The following sequences was taken from the BEDROCK HIV Problem Space Database, from the Markham et al. (1998) study. The sequence were compiled into a single text document in FASTA format:
- AIDS
- 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)
- Subject 3
- Progressing Towards AIDS
- 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)
- Subject 8
- No Trend
- 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)
- Subject 5
- AIDS
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:
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.
