From 16S to genome

[Krosh]

I have a lot of 16S rRNAs ID and it is necessary to obtain whole bacterial genomes if it exists or all bacterial genes (ID or fasta).
Is it possible to automate?

[rhinoceros]

What IDs do you have? GIs?

[Krosh]

Yes, Gene IDs

[rhinoceros]

So basically you need to link GIs to NCBI taxon IDs. I think NCBI might even maintain such a file in their FTP. Otherwise, use eutils..