[ensembl-dev] Coordinate System anomalies in EnsemblGenomes

Dan Staines dstaines at ebi.ac.uk
Mon Mar 4 11:43:03 GMT 2013

On 03/04/2013 11:33 AM, PATERSON Trevor wrote:
> I think that my temporary crisis in comprehension is due to a
> particular problem with the bacterial assembly example given,  all
> 244 of the sequence regions labelled as top level (with coordsystem
> = 'supercontig') seem to be identical to the 244 sequence regions
> belonging to the sequence_level coord system ('contig') - so it
> appears that in fact  no "assembly" has been imported into
> ensemblgenomes for this species.

For the pipeline used for bacteria, we only use set of sequences which 
equate to the highest level of assembly we can find (chromosomes or 
supercontigs). Following Ensembl convention, we separate features and 
sequences onto different coordinate systems which means we get two 
identical sets of seq_regions, one of which is toplevel (and hence has 
features) and one of which has the sequence attached via the DNA table - 
this has always been the case for bacteria and has remained the same.


Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/

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