Alex A. Cardenas Week 3: Difference between revisions
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==Methods== | ==Methods== | ||
*Started by uploading the "visit_1_S1_S9.txt" and "visit_1_S10_S15.txt" into workbench | *Started by uploading the "visit_1_S1_S9.txt" and "visit_1_S10_S15.txt" into workbench | ||
*Picked 12 sequences out of the 97. | |||
Subject Clone | |||
1 1 | |||
1 4 | |||
1 7 | |||
2 1 | |||
2 4 | |||
2 6 | |||
9 1 | |||
9 3 | |||
9 5 | |||
14 2 | |||
14 5 | |||
14 6 | |||
Revision as of 15:25, 14 September 2011
Activity 1
Methods
- Went to pubmed to find the Markham paper
- Clicked on nucleotide under the links to find the sequences
- Retrieved the sequence file S4V2-4 and viewed it in the FASTA format
- Which was then copy and pasted into Biology workbench.
- Copy and pasted sequences into a txt. file saved it as 'sequence.txt'
- Uploaded all of the files and then ran them all using ClustalW
- After running the program and sequences compared, the scores were:
Sequences (1:2) Aligned. Score: 86 Sequences (1:3) Aligned. Score: 85 Sequences (1:4) Aligned. Score: 97 Sequences (1:5) Aligned. Score: 97 Sequences (2:3) Aligned. Score: 97 Sequences (2:4) Aligned. Score: 84 Sequences (2:5) Aligned. Score: 84 Sequences (3:4) Aligned. Score: 83 Sequences (3:5) Aligned. Score: 84 Sequences (4:5) Aligned. Score: 96
- The unrooted tree was
Questions
- What was the accession number of the sequence you chose?
- AF016818
- Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from?
- Subject 2 visit 4
- Envolope glycoprotein region V3 (env) gene
Activity 2
Methods
- Started by uploading the "visit_1_S1_S9.txt" and "visit_1_S10_S15.txt" into workbench
- Picked 12 sequences out of the 97.
Subject Clone 1 1 1 4 1 7 2 1 2 4 2 6 9 1 9 3 9 5 14 2 14 5 14 6
