I would like to discuss the type of strategies you use for whole genome annotation. I am not restricting the question to the organisms I am currently working on, but I have been working on herpesviruses, which have quite small genes (from 100bp to 10,000bp) and only a few contain introns. Fortunately, contrary to small RNA viruses, in herpesviruses (dsDNA), few genes are overlapping.
What is your experience in genome annotation and what are the tools/strategies you would favor?
Thanks in advance for the discussion.