I am looking for a software to do pfam enrichment analysis for my differential expressed genes from RNAseq. I have the differentially expressed gene list, and the annotaiton (GO, pfam, KEGG) of the genes in the genome. I did the GO enrichment analysis using GOseq. However, Goseq cannot do pfam. I wonder if there is a similar software for any annotation term that I want to analyze, particularly pfam.
The species I am working on is not model species. So I am looking for a software that allows me to upload my own annotation file.
Thank you very much.