[ensembl-dev] pseudogenes in ensembl bacteria

Adam Witney awitney at sgul.ac.uk
Wed Aug 21 15:42:49 BST 2013

On 21. 8. 2013 15:40, Dan Staines wrote:
> On 08/21/2013 03:37 PM, Adam Witney wrote:
>> Thanks for that Dan. Are the pseudogene labels stored anywhere in the
>> database? ie the label HI_0006 in haemophilus_influenzae_rd_kw20.fa is
>> not present, but I guess it is one of the gene_feature's at the bottom.
> No, unfortunately they're not - these are the same as the locus_tags
> which I mentioned in my mail above. If I'm able to reload these genes
> using the updated pipeline, its possible that I'll be able to generate a
> lookup list for you if thats a help in the short term.

Actually it looks like they are generally within the 
$simple_feature->display_label() field, but in some cases this seems to 
have been truncated? e.g. gene_feature:1633

Thanks again


More information about the Dev mailing list