<br><br><div class="gmail_quote">On Wed, Feb 23, 2011 at 12:42 PM, PATERSON Trevor <span dir="ltr"><<a href="mailto:trevor.paterson@roslin.ed.ac.uk">trevor.paterson@roslin.ed.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Ta thats very helpful<br>
<br>
1) I take it species.division isn't listed for <a href="http://ensembl.org" target="_blank">ensembl.org</a> databases because they all belong to the 'multi' group.<br>
<br>
2) Regards the second point: I don't think each compara database contains pairwise comparisons between all members<br>
<br>
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<br>
<br>
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....<br></blockquote><div><br>Orthology / paralogy predictions are done between all species of a database. Genomic alignments only between certain combinations of species.<br>
<br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
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...<br></blockquote><div><br>You can find the list here:<br>
<br><a href="http://metazoa.ensembl.org/info/docs/compara/homology_method.html">http://metazoa.ensembl.org/info/docs/compara/homology_method.html</a><br><br>(end of page) <br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Thanks again<br>
<div class="im"><br>
Trevor Paterson PhD<br>
email <a href="mailto:trevor.paterson@roslin.ed.ac.uk">trevor.paterson@roslin.ed.ac.uk</a><br>
<br>
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</div><div><div></div><div class="h5">-----Original Message-----<br>
From: Dan Staines [mailto:<a href="mailto:dstaines@ebi.ac.uk">dstaines@ebi.ac.uk</a>]<br>
Sent: 23 February 2011 12:30<br>
To: PATERSON Trevor<br>
Cc: '<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>'<br>
Subject: Re: [ensembl-dev] ensemblgenomes compara databases<br>
<br>
<br>
<br>
On 02/23/2011 12:22 PM, PATERSON Trevor wrote:<br>
> 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].<br>
<br>
yes, this is in the meta table as "species.division" e.g.<br>
"EnsemblMetazoa". You could use this to work out which division-specific compara db to use.<br>
<br>
> 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).<br>
<br>
Not sure what you mean here - can you give me an example of what you need to do?<br>
<br>
> Also what is the compara_pan database?? - the contents of all the other databases??<br>
<br>
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).<br>
<br>
Dan.<br>
<br>
--<br>
Dan Staines, PhD Ensembl Genomes Technical Coordinator<br>
EMBL-EBI Tel: +44-(0)1223-492507<br>
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468<br>
Cambridge CB10 1SD, UK <a href="http://www.ensemblgenomes.org/" target="_blank">http://www.ensemblgenomes.org/</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bert Overduin, Ph.D.<br>Vertebrate Genomics Team<br><br>EMBL - European Bioinformatics Institute<br>Wellcome Trust Genome Campus<br>Hinxton, Cambridge CB10 1SD<br>
United Kingdom<br><br><a href="http://www.ebi.ac.uk/%7Ebert" target="_blank">http://www.ebi.ac.uk/~bert</a><br>