Functional annotation by blast
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11 weeks ago
pooryamb • 0

Dear all,

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.

trembl Blast nr Functional_annotation Blast2GO • 242 views
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TrEMBL also contains computationally translated genes. If you want curated genes then you should look at UniProt of RefSeq proteins.

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Thanks for your reply. I think for some of the genes that are in TrEMBL, automatic electronic functional annotation is available. So, I guess if I blast against TrEMBL (rather than UniProt), I will get some new hits. But, I am not sure whether the genes in nr but not in TrEMBL have any automatic electronic functional annotation or not?