I would like to do gene ontology annotation of a set of proteins from a non-model organism. I have been using BLAST2GO, mainly because it allows me to merge GO terms from the "mapping" step with those from InterProScan quite easily. However, it conducts web-based InterProScan and so is very slow. It seems that the free version of BLAST2GO does not allow me to import .xml result file from InterProScan v5.x (only .xml output from InterProScan v4.8), so I cannot run InterProScan separately. Because my organism of interest is pretty distant from mammals, InterProScan results are quite useful.
Is there a way to conduct GO mapping both through BLAST-based and InterProScan-based approaches, and then merge the GO terms for each gene?
Thank you very much!