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Ellior2 / Fish-546-Bioinformatics

Fall 2016 Class Repo
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Point on Project #6

Open sr320 opened 7 years ago

sr320 commented 7 years ago

My goal is to characterize a Pacific oyster (Crassostrea gigas) proteome for this class. Potential first steps: 1) Gain a full understanding of what my dataset represents. 2) Use Blast to identify matched proteins between a database and our query. 3) Further research the functions of these identified proteins. I eventually will be analyzing differences in proteomes between P. oysters reared under different conditions so I think this will be important in getting "baseline" data or just familiar with different types of proteins that are typically expressed in these oysters.

Good first steps. Your main initial steps will be Blast. You will need to devise means to blast on locations not on your laptop (while still documenting fully on in your repo).

Start by getting set up on a lab desktop, then determine options on Cyverse

Ellior2 commented 7 years ago

At this point I am just fiddling around with things. I am not quite sure what database I should be using for the Blast. I tried doing a BlastP using my query file and the Uniprot database that we used for the tutorial since my query data are proteins, not nucleotides sequences. Am I in the right direction?

Notebook

sr320 commented 7 years ago

Yes, you should a Blastp job started to compare to Uniprot.

On Wed, Oct 19, 2016 at 2:48 PM Rhonda Elliott notifications@github.com wrote:

At this point I am just fiddling around with things. I am not quite sure what database I should be using for the Blast. I tried doing a BlastP using my query file and the Uniprot database that we used for the tutorial since my query data are proteins, not nucleotides sequences. Am I in the right direction?

Notebook https://github.com/Ellior2/Fish-546-Bioinformatics/blob/master/notebooks/classproject/001-BlastingProject.ipynb

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