Alex J. George Week 4: Difference between revisions
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* Goal: Determine if the isolated HIV from subgroups comes from a common source | * Goal: Determine if the isolated HIV from subgroups comes from a common source | ||
* Multiple sequence alignment: comparing nucleotide positions for many sequences | * 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==== | ====Part 1: Clustering across subjects==== | ||
* Selected Sequences: | * Selected Sequences: | ||
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S9V1-5 | S9V1-5 | ||
* Resulting Unrooted Tree: | |||
{{Alex J. George}} | {{Alex J. George}} |
Revision as of 12:39, 9 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:
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