I've got a couple of questions using Prokka.
1) anybody come across the problem of annotating small ORFs? Lots of operon leader peptides etc remain un-annotated. I understand that's to reduce the false positives, but I still would want to annotate these genes.
2) how does one compile a good genus-specific database? E.g. if I need a reference protein set for Salmonella, what is a good strategy?
Thank you in advance.