Is there any fast and reliable way to annotate protein sequences from bacterial genomes to the GO terms?
The best option so far seems to install and run a local copy of InterproScan, but its annotations go way beyond my needs and its computationally very expensive. Also, there doesn't seem to be a way to speed-up the analysis to obtain just the GO-terms. Maybe reducing the number of inspected DBs?
Any other tool/database that perform an annotation in reasonable time would be fine.
Update: turned out that iprscan version 5 is less aggressive and a bit faster than previous versions: the annotation of ~10'000 proteins took a little more than one day.