Alex A. Cardenas Week 3: Difference between revisions
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| Line 1: | Line 1: | ||
=Activity 1= | |||
==Methods== | ==Methods== | ||
*Went to pubmed to find the Markham paper | *Went to pubmed to find the Markham paper | ||
| Line 17: | Line 18: | ||
Sequences (3:5) Aligned. Score: 84 | Sequences (3:5) Aligned. Score: 84 | ||
Sequences (4:5) Aligned. Score: 96 | Sequences (4:5) Aligned. Score: 96 | ||
*The unrooted tree was | *The unrooted tree was (Picture) | ||
Questions | Questions | ||
*What was the accession number of the sequence you chose? | *What was the accession number of the sequence you chose? | ||
| Line 24: | Line 25: | ||
**Subject 2 visit 4 | **Subject 2 visit 4 | ||
**Envolope glycoprotein region V3 (env) gene | **Envolope glycoprotein region V3 (env) gene | ||
=Activity 2= | |||
Revision as of 14:46, 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 (Picture)
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
