Alex J. George Week 4: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
(Unrooted tree uploaded) |
No edit summary |
||
Line 37: | Line 37: | ||
* Resulting Unrooted Tree: [[Media:Unrooted Tree- V1-S1,S7,S8,S9-Clones3,4,5.pdf]] | * Resulting Unrooted Tree: [[Media:Unrooted Tree- V1-S1,S7,S8,S9-Clones3,4,5.pdf]] | ||
* The clones from each subject do cluster together, but none of the subjects cluster together. They seem to be all equally diverse from the other subjects. | |||
* The clones from Subject 7 definitely show more diversity than the other subjects. Subject 9 shows the least diversity between clones. | |||
* My tree shows that all of the subjects are equally distinct from the others. Subject's 8 clones 3 and 4 are nearly identical to each other, overlapping on the tree. This most likely indicates a minor mutation between the two clones. | |||
====Part 2: Quantifying Diversity==== | |||
* S= number of positions that vary | |||
{{Alex J. George}} | {{Alex J. George}} |
Revision as of 15:38, 13 February 2010
Activity 1: Searching NCBI
Part 2: Genbank
- Accessed Genbank records from the right-hand links of the Pubmed version of the article.
- Accession Number of sequence: AF016767.2
- This sequence was taken from the first visit of Subject 1. This information is given in the title of the sequence.
Part 3: Biology Workbench
- Registered for Workbench, followed "Nucleic Tools" link to add a sequence.
- Uploaded sequences successfully, realizing it is best to keep the file saved as a ".fasta" file
- CLUSTALW Tool performs multiple sequence alignment on protein or nucleic sequences
- Example: gi:33187149 and gi:33187151 are on the same side of the tree because their differences from the other sequences are most similar. For example, in the 21st and 22nd base pairs, these sequences show "AA" whereas the other three show "CC"
Activity 2: Looking at sources of HIV across subjects
- Goal: Determine if the isolated HIV from subgroups comes from a common source
- Multiple sequence alignment: comparing nucleotide positions for many sequences
- Unrooted Trees:
- Represent genetic distance b/t pairs of sequences--> Total length b/t nodes represents genetic distance between 2 sequences
- B/c unrooted- can't make inferences about direction of evolutionary change
- Long internal branches separate clusters of sequences that a dissimilar
Part 1: Clustering across subjects
- Selected Sequences:
Selected Sequence(s) S1V1-3 S1V1-4 S1V1-5 S7V1-3 S7V1-4 S7V1-5 S8V1-3 S8V1-4 S8V1-5 S9V1-3 S9V1-4 S9V1-5
- Resulting Unrooted Tree: Media:Unrooted Tree- V1-S1,S7,S8,S9-Clones3,4,5.pdf
- The clones from each subject do cluster together, but none of the subjects cluster together. They seem to be all equally diverse from the other subjects.
- The clones from Subject 7 definitely show more diversity than the other subjects. Subject 9 shows the least diversity between clones.
- My tree shows that all of the subjects are equally distinct from the others. Subject's 8 clones 3 and 4 are nearly identical to each other, overlapping on the tree. This most likely indicates a minor mutation between the two clones.
Part 2: Quantifying Diversity
- S= number of positions that vary
Individual Journals
- No Week 1 Journal
- Alex J. George Week 2
- Alex J. George Week 3
- Alex J. George Week 4
- Alex J. George Week 5
- Alex J. George Week 6
- Alex J. George Week 7
- Alex J. George Week 8
- Alex J. George Week 9
- Alex J. George Week 10
- Alex J. George Week 11
- Alex J. George Week 12
- Alex J. George Week 13