the first way is using nr databases to annotate the sequences, and then use those ids to get GO annotation and statistics the second way is as blast2go to do any one can tell me a pipeline to do GO analysis thank u -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253