I have annotated a set of proteins with BLAST2GO. I've also annotated the complete proteome of the same specie. Now i want to check for enriched GO terms in my protein set compared to the whole proteome.
The BLAST2GO fischer exact test feature isn't working correctly (i guess) because it excludes proteins from the reference set that are also present in the test set.
I've checked multiple tools, DAVID and ontologizer for example, but i can't find an appropriate one. ArgriGO seems to accept custom annotations but has an upload limit of 4 MB which is to low for my data set.
Any help is appreciated!!
Thank you in advance,