How To Retrieve Upstream Sequences Of A Single Gene From Multiple Bacterial Species?

Question

[Magdalena]

I am looking for an efficient way of retrieving the upstream flanking regions of a specific gene which is present in many bacterial species. The homologs share the same name, so that should be easy. I tried using Biomart (which I have practically no experience with) but there it seems I can only retrieve sequences from one database/species at a time.

When I search for the gene name in NCBI I get all results that I want but I don't know how to automatize retrieving the upstream regions.

Thank you.

Answer 1

[Davy]

IF you are familiar with Perl the eutils should be able to sort you out.

http://www.ncbi.nlm.nih.gov/books/NBK25501/

Answer 2

[Manu Prestat]

Look at my answer here: This should be almost the same.