Zrusso Biol 368 week 3: Difference between revisions
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*uploaded all the subject sequences first into .txt files and then into bio workbench | *uploaded all the subject sequences first into .txt files and then into bio workbench | ||
*Did a preliminary analysis of three sequences from 4 different subjects as an unrooted tree | *Did a preliminary analysis of three sequences from 4 different subjects as an unrooted tree | ||
[[ | [[image:10307.CLUSTALW.1.jpg]] | ||
==Week 4 Journal Club Prep== | ==Week 4 Journal Club Prep== | ||
{{Zrusso Biol 368}} | {{Zrusso Biol 368}} | ||
Revision as of 14:41, 14 September 2011
Exploring HIV Evolution Electronic Notebook
- Found in the article the GenBank Accession numbers, but it only lists the first and last of the groups of sequences, so it only lists four sequences
- can navigate among the sequences by changing the URL, but as far as I can tell, there is no way to just go between the different sequences from the paper.
- I chose GenBank Accession number AF016821
- It says right in the title that it was taken from subject 2, visit 4, clone 5 from the USA
- Downloaded 5 FASTA sequences to a single word doc for use in the biology workbench
- created a bio workbench userID and attempted to input my sequences but using the browse and upload buttons would kick me back to the homepage, so instead I just manually copied and pasted the sequences in.
- performed a clustalW multiple sequence alignment on the 5 sequences to get an idea of how closely related they are
- rooted tree diagram of my 5 sequences
- multiple sequence alignment
- created new session for the subject HIV cross examination
- uploaded all the subject sequences first into .txt files and then into bio workbench
- Did a preliminary analysis of three sequences from 4 different subjects as an unrooted tree
