Question: How To Retrieve Upstream Sequences Of A Single Gene From Multiple Bacterial Species?
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gravatar for Magdalena
7.4 years ago by
Magdalena0
Magdalena0 wrote:

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.

ADD COMMENTlink modified 7.4 years ago by Manu Prestat3.9k • written 7.4 years ago by Magdalena0
0
gravatar for Davy
7.4 years ago by
Davy210
Davy210 wrote:

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

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

ADD COMMENTlink written 7.4 years ago by Davy210
0
gravatar for Manu Prestat
7.4 years ago by
Manu Prestat3.9k
Marseille, France
Manu Prestat3.9k wrote:

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

ADD COMMENTlink written 7.4 years ago by Manu Prestat3.9k
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