Go enrichment analysis- blastp uniprot

Question

[S20]

Hi All, I am trying to perform GO enrichment analysis, for the first time so I am not familiar with the process. I read many of questions/answers and papers but now I'm really confused of I need to do. Any helps would be appreciated.

I have a list of genes from a plant species and I need to do GO enrichment analysis. What I've done so far are;

1) I try blast2go which was super slow so I gave up on that.

2) I also need the Go terms for whole genome to use as a reference/background for enrichment analysis. So first, I run the whole genome through interproscan and get the Go term for some of the genes by --goterms option, not all of the genes have GO term. I think the next step is blasting against uniprot to get GO term? if so how I can perform that? do I need to download uniprot database?

Thanks in advance for your help!

Answer 1

[shelkmike]

I recommend to use PANNZER2 for GO annotation. It is a high quality program which works faster than Blast2GO. For GO enrichment I recommend GOATOOLS - it is quite simple but efficient.