software for gene ontology - (Dec/15/2009 )

is there any suggestion for software use for functional annotation beside blast2Go? for ur information, i got 500 sequences for functional annotation. i try to run blast2Go for both gene prediction and functional annotation. but it only manage to run gene prediction. so may be u guys got better suggestion for that? thanks a lot

You could try DAVID from the U.S. National Cancer Institute....though the website seems be down at the moment. Here's a 'How-to' paper from Nature Genetics that describes the statistical basis and ontology organization strategies. Best of all...it's free.

+1 for DAVID.
The author is usually quick in answering your email or forum post.

BTW, that How-to paper is not really that good. Many terms are still not explained well and as all other programs help file is outdated. You will need some time to get hang of it (if you want most out of that program)