How to annotate genomes downloaded from NCBI?

Question

[arosa]

In addition: is it possible to reduce the annotation to specific genes only? My aim with this is to retrieve protein sequences from poorly annotated genomes.

[GenoMax]

NCBI does not have annotation for these? Can you post an example accession #? If no annotation exists then there is no magic bullet but to do it yourself.

[lieven.sterck]

What kind of 'specific genes' do you mean, like with a certain function or description? but I'm guessing it's more on a structural level?