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<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">For example, Pseudomonas aeruginosa:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><a href="http://bacteria.ensembl.org/Pseudomonas_aeruginosa/Info/Index">http://bacteria.ensembl.org/Pseudomonas_aeruginosa/Info/Index</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The GFF3 link points to:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><a href="ftp://ftp.ensemblgenomes.org/pub/bacteria/release-40/gff3/bacteria_67_collection/pseudomonas_aeruginosa/Pseudomonas_aeruginosa.PUPa3_1.0.40.abinitio.gff3.gz">ftp://ftp.ensemblgenomes.org/pub/bacteria/release-40/gff3/bacteria_67_collection/pseudomonas_aeruginosa/Pseudomonas_aeruginosa.PUPa3_1.0.40.abinitio.gff3.gz</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">..but all of the entries in that file are contigs. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The genome contains gene annotations though:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><a href="http://bacteria.ensembl.org/Pseudomonas_aeruginosa/Location/View?r=contig47.2%3A320186-324631;site=ensemblthis">http://bacteria.ensembl.org/Pseudomonas_aeruginosa/Location/View?r=contig47.2%3A320186-324631;site=ensemblthis</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">..how do I get the positions and annotations of the genes?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Simon.<o:p></o:p></p>
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