[ensembl-dev] EPO generated ancestral genome ever used by ensembl browser?

[Javier Herrero]

Hi Sharon

Yes, the ancestral sequences are (can be) displayed on the gene sequence view, 
alignment view (both text and graphical displays) from the Location tab and 
the phylogenetic context view in the SNP tab.

In the MULTI.ini file, you need an entry for the ancestral DB in the 
[databases] section:

[databases]
DATABASE_CORE    = ensembl_ancestral_%
DATABASE_COMPARA = ensembl_compara_%
DATABASE_GO      = ensembl_ontology_%

On a related note, the ancestral sequences are the basis of the ancestral 
allele calls for the human SNPs in the forthcoming dbSNP release.

Javier

On Monday 01 Nov 2010 19:14:42 Sharon Wei wrote:
>   Dear Ensembl team,
> 
> I have an ancestral genome created from running EPO pipeline. I am
> curious whether ancestral core dbs are ever used in any of the views on
> ensembl genome browser. If yes, how should I configure the web server to
> connect to the ancestral db?
> 
> Thanks,
> 
> 
> Sharon
> Cold Spring Harbor Labs
> 
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-- 
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK