[ensembl-dev] Downloading annotation from Ensembl

[Greg Slodkowicz]

Hi Fiona,

> 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
>

Thanks for getting back to me. I've previously downloaded the GTF
file under "Gene sets" but it seems that it contained coordinates of genes,
exons and CDS but not other functional features such as domains, secondary
structure predictions etc..  Is this the file you're referring to?


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

They're sitewise predictions of evolutionary constraint, very similar to
those from
http://www.nature.com/nature/journal/v478/n7370/abs/nature10530.html.

Best,
Greg

-- 
Greg Slodkowicz
PhD student, Nick Goldman group
European Bioinformatics Institute (EMBL-EBI)
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