Goal:

Create a pangenome of SAR11 and see all the transport and catabolic genes related to metabolite utilization.

It would inform me of all the common gene clusters of all known SAR11 genomes and see how diverse their diet is.

This website provides some guidance: https://merenlab.org/2016/11/08/pangenomics-v2/

#Week 4/7: Notes from Meeting with Steven

Data:Found four genomes from NCBI that are full genomes of cultured data. Morris Lab is also providing two genomes that have not been published. What genes are present, multiple copies, the unique genes?

Downloading through curl the complete genomes and acquire the annotations.

I am bit confused about HASH??

goal: presense and absence of genomes.

#Week 4/14: Workflow:

Identify genomes working with. a. From NCBI: 4 full genomes of Candidatus Pelagibacter and 2 genomes from own lab. b. annotated genomes, looking into the protein sequences and other annotations.
Run BLAST. a. Using week 1 code run blasts on all genomes. b. provides information about the genomes.
Identifies differences and similarities. a. I think this is the ultimate goal where you can find the differences and similarities on a table. Maybe using the proteins could indicate more metabolite utilization.