If you're working with humans you can get a nicely annotated, sort of biologically relevant FASTA database from just about anywhere.
Will it lack virtually all common genetic variants? Yes
Will it lead you to think that some proteins are down regulated when it's just that you're not doing proteomics on the one Caucasian dude that the vast majority of the sequences came from? Again yes.
But it is easy to work with.
What if you want to work with something less easy?
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