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3.0 years ago
ja4123
▴
20
Hey! Question as in the title. Can someone give some advice or suggest some biopython functions? Kindly help.
1
Entering edit mode
3.0 years ago
GenoMax
141k
Why does it have to be biopython? When you have specific requirements like that you should make a note of why that is so.
Otherwise see the solutions in: How to download all Pseudomonas aeruginosa Genomes from NCBI Genomes database?
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Thanks for the answer! For example I need 100 randomly selected Bacteria from UniProt, it would be hard to do it by hand.
Proteomes listed on UniProt site for bacteria appear to be in a random order. You could simply take the first 100. See "non-redundant" and "non-excluded" filters at top of page to further refine the selections.
It is possible to do the same using PDB?
PDB has individual structures of proteins. Are you referring to random individual proteins?
Less by PDB. Going back to the example (100 randomly selected bacteria) in the link you put in there is a download option (you can select 100) but there is no sequence information in what you can download.
You will need to click through on an entry until you get to page (example LINK) where you can select all proteins and download them as fasta file.
Better option: You should be able to download the proteomes from UniProt's FTP site. Here is the page for bacteria. A random example of protein fasta.