I'm attempting to convert my collection of scattered annotations into a unified GenBank Flat File. I've been looking at how different programs interact with the format, ranging from only accepting a set of the feature types, while others arbitrarily shoehorn the data into a feature type, and still others simply use the feature type as a sort of analog XML for loading their annotations in and out.
Is there a "Right" way to use the GB format?
I've seen the GFF format, but the GFF3 specification separates annotation data from sequence data. This is really good for big, abstracted data models, but isn't what I'm looking for at the moment because I still need to be able to convey that linkage to myself when I read my own data. Am I wrong to avoid GFF for this reason? What are other file formats I should look at?