[ensembl-dev] GFF files for bacterial genomes

Simon Andrews simon.andrews at babraham.ac.uk
Wed Jul 18 15:56:37 BST 2018


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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