[ensembl-dev] ensemblgenomes compara databases

Dan Staines dstaines at ebi.ac.uk
Wed Feb 23 12:29:54 GMT 2011

On 02/23/2011 12:22 PM, PATERSON Trevor wrote:
> Do the individual core databases contain information about which group the species belongs to? [it would be nice if this was listed in 'meta' table].

yes, this is in the meta table as "species.division" e.g. 
"EnsemblMetazoa". You could use this to work out which division-specific 
compara db to use.

 > And is meta data stored about which species are used in pairwise 
comaprisons in each compara database (without having to query the 
compara database for which genome databases it references).

Not sure what you mean here - can you give me an example of what you 
need to do?

 > Also what is the compara_pan database?? - the contents of all the 
other databases??

Pan compara is a peptide compara database produced from a set of 
selected species that are taken from all EnsemblGenomes divisions and 
from Ensembl (but doesn't include all species from all divisions).


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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