GO for novel species

Question

[vipulbatra.pu]

I have a list of Entrez gene IDs for Buffalo and would like to do GO and pathway analysis. However, none of the GO analysis tools has buffalo in their organisms'' list. DAVID does help up to an extent, nevertheless, almost 50% of the genes were unmapped. This is the only tool that recognizes my gene IDs. How to proceed further? Any help would be highly appreciated.

[Mehmet]

Have you checked Blast2GO for GO analysis? You can give DNA or protein sequences of your novel species as input to Blast2GO. Blast2Go uses multiple sources (interpro, PFAM etc) and map to GO term also gives PFAM ids for PFAM domain and description. Using GO given by Blast2GO you can perform GO enrichment with topGO R package if you want.