Download uniprot protein database

Question

[elena.syp]

Hi!

I want to download the full set of uniprot proteins from vertebrates to use to annotate my de novo transcriptome. I can only find proteomes per species, but I don't see anywhere a file containing a pull of proteins for all vertebrates. Can somebody tell me if that exist and where to find it? Thanks a lot

Answer 1

[GenoMax]

Complete UniProt database is available via their FTP site. If you only need vertebrate proteins then you may need to parse those out or perhaps use the web advanced search (will take a look to see if that is feasible).

Update: You could do this search via web. Then click on the download button and then choose Download All--> Fasta compressed to save a file locally.