[ensembl-dev] GFF files for bacterial genomes

James Allen jallen at ebi.ac.uk
Fri Jul 20 17:01:21 BST 2018


Hello,
Thank you for bringing this to our attention; it looks like our GFF dumping failed here. We will generate the files and update the ftp site, but in the meantime you can use files from release 37 (which seems to be the most recent release with a full set of GFF files - and the assemblies/genesets have not been updated since then): ftp://ftp.ensemblgenomes.org/pub/bacteria/release-37/gff3

Regards,
James
Ensembl Production


On Wed, 18 Jul 2018 14:56:37 +0000
Simon Andrews <simon.andrews at babraham.ac.uk> wrote:

> I'm trying to get hold of GFF files for genomes in the bacterial
> enesmbl section.  For all of the strains I've looked at I can see the
> genome sequence, and there is a link to the GFF annotation file, but
> there is never any gene annotation in it.  The only things I see are
> contig positions.
> 
> For example, Pseudomonas aeruginosa:
> 
> http://bacteria.ensembl.org/Pseudomonas_aeruginosa/Info/Index
> 
> The GFF3 link points to:
> 
> ftp://ftp.ensemblgenomes.org/pub/bacteria/release-40/gff3/bacteria_67_collection/pseudomonas_aeruginosa/Pseudomonas_aeruginosa.PUPa3_1.0.40.abinitio.gff3.gz
> 
> ..but all of the entries in that file are contigs.
> 
> The genome contains gene annotations though:
> 
> http://bacteria.ensembl.org/Pseudomonas_aeruginosa/Location/View?r=contig47.2%3A320186-324631;site=ensemblthis
> 
> ..how do I get the positions and annotations of the genes?
> 
> Thanks
> 
> Simon.
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