I am working on annotating a bacterial genome and this is my first time doing so. I got the genes in the genome but am starting to look at intergenic regions. Any suggestions on good programs for identifying RNAs and promotor sequences?
Are you planning to submit this, I'm assuming newly sequenced genome, to one of the big databases (e.g. NCBI)? If so then you should definitely ask to get access to their annotation tools [?]here[?]
Otherwise, there are quite a few tools out there. Here are some of them:
http://linux1.softberry.com/berry.phtml (specifically [?]BPROM[?])
[?]BacPP is another one[?]
Hope this helps