[ensembl-dev] pseudogenes in ensembl bacteria

[Dan Staines]

On 08/20/2013 11:03 AM, Adam Witney wrote:
>
> Are details about pseudogenes stored anywhere? For example, HI_0006 from
> haemophilus_influenzae_rd_kw20 seems to be missing from any of the
> downloaded files (fasta, gff3, gtf) and is not searchable on the
> browser. Can it be accessed (i.e coordinates and DNA sequence) from any
> of the database tables?

We do store pseudogenes in the gene and transcript table with biotype 
pseudogene where there are gene features marked as /pseudo in the 
original INSDC record. I'll look into this particular example and let 
you know.

-- 
Dan Staines, PhD
Technical Coordinator, Ensembl Genomes
European Bioinformatics Institute (EMBL-EBI)
http://www.ebi.ac.uk/
http://www.ensemblgenomes.org/