I would like to fetch specified genomic regions from refseq genomes without having to download the full genome.
The regions are previously identified with a hmmer search. To my understandment Ensembl does not have all Refseq genomes.
One thing to be aware of : If you use a top level RefSeq accession for bacterial genomes there may be multiple plasmids etc in that accession. Sequences may be retrieved from those as well. You may need to eliminate some of those sequences (example below).