[ensembl-dev] ensemblgenomes compara databases

[Bert Overduin]

On Wed, Feb 23, 2011 at 12:42 PM, PATERSON Trevor <
trevor.paterson at roslin.ed.ac.uk> wrote:

>
> Ta thats very helpful
>
> 1) I take it species.division isn't listed for ensembl.org databases
> because they all belong to the 'multi' group.
>
> 2) Regards the second point: I don't think each compara database contains
> pairwise comparisons between all members
>
> For example in bacteria a cursory examination suggests that all members of
> the ecoli collection are compared with each other - but not with members of
> the bacillus collection
>
> So, in the case of no homology being found for a gene,  I think you have to
> pull out the species_sets to know whether a comparison was done....
>

Orthology / paralogy predictions are done between all species of a database.
Genomic alignments only between certain combinations of species.


> 3) In  the Pan compara database - I take it you just need to look and see
> which species are in it (in genome_db), to know whether you can search a
> species for homologies...
>

You can find the list here:

http://metazoa.ensembl.org/info/docs/compara/homology_method.html

(end of page)

>
> Thanks again
>
> Trevor Paterson PhD
> email trevor.paterson at roslin.ed.ac.uk
>
> Bioinformatics
> The Roslin Institute
> The Royal (Dick) School of Veterinary Studies
> University of Edinburgh
> Scotland EH25 9PS
> phone +44 (0)131 5274197
> http://bioinformatics.roslin.ed.ac.uk/
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> -----Original Message-----
> From: Dan Staines [mailto:dstaines at ebi.ac.uk]
> Sent: 23 February 2011 12:30
> To: PATERSON Trevor
> Cc: 'dev at ensembl.org'
> Subject: Re: [ensembl-dev] ensemblgenomes compara databases
>
>
>
> 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.
>
> --
> 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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-- 
Bert Overduin, Ph.D.
Vertebrate Genomics Team

EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

http://www.ebi.ac.uk/~bert
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