[ensembl-dev] Downloading annotation from Ensembl

Fiona Cunningham fiona at ebi.ac.uk
Tue Jan 21 13:57:46 GMT 2014


Hi Greg,

We do have GTF files for our gene annotations. You can see a table of all
our download files here:
http://www.ensembl.org/info/data/ftp/index.html

What are your features? If they are variation data you could use our
variant effect predictor (VEP) http://www.ensembl.org/VEP.

Best wishes,


Fiona

---------------------------------------------------------------------------------------------------------------
Fiona Cunningham, Ensembl Coordinator, Ensembl Variation Project Leader.
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton,  CB10 1SD, UK
www.ensembl.org || www.lrg-sequence.org || t: +44 1223 494612


On 17 January 2014 11:50, Greg Slodkowicz <gregs at ebi.ac.uk> wrote:

> Hi Ensembl-dev
> I would like to correlate some features I calculated with existing
> annotation such as secondary structure and presence of domains.  I was
> wondering if there's a way to download the annotation from Ensembl as
> genome browser tracks or GTF files?  I poked around the FTP a little bit
> but could only find the MySQL dumps.  Is this the only way to go?
>
> Best,
> Greg
>
> --
> Greg Slodkowicz
> PhD student, Nick Goldman group
> European Bioinformatics Institute (EMBL-EBI)
>
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