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

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.

retrieval homology bacteria biomart
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updated by Manu Prestat Manu Prestat • written by Magdalena • Magdalena

2 answers

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

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

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written by Davy Davy

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

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updated by Ram Ram • written by Manu Prestat Manu Prestat

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