I want to annotate 11,000 genes with Blast2GO. For this, I have to run Blast for all of the genes (on a standalone server). I wondered whether I might lose anything if I blast my genes against TrEMBL (rather than nr). I feel like the genes in NR but not in TrEMBL do not have functional annotation, so it is useless to blast against them. But I am not sure.
I really appreciate any help you can provide.