[ensembl-dev] Sus scrofa is not a valid species name?

Dan Staines dstaines at ebi.ac.uk
Thu Jun 21 20:49:41 BST 2012

> database    escherichia_collection_core_14_67_5
> species/group    e_coli_se11/core
> species/group    e_coli_o127_h6/core
> species/group    e_coli_o17_k52_h18/core
> species/group    e_fergusonii/core
> species/group    e_coli_55989/core
> species/group    e_coli_o8/core
> species/group    e_coli_o45_k1/core
> species/group    e_coli_o81/core
> species/group    e_coli_o7_k1/core
> species/group    e_coli_bw2952/core
> species/group    e_coli_bl21/core
> species/group    e_coli_rel606/core
> species/group    e_coli_tw14359/core
> species/group    e_coli_o26_h11/core
> species/group    e_coli_o103_h2/core
> species/group    e_coli_o111_h_/core
> species/group    e_coli_bl21_de3_kribb/core
> species/group    e_coli_atcc_33849/core
> species/group    e_coli_bl21_de3_jgi/core
> species/group    s_flexneri_x/core
> species/group    e_coli_se15/core
> species/group    e_coli_042/core
> species/group    e_coli_o55_h7/core
> species/group    e_coli_o157_h7_tw14588/core
> species/group    e_coli_o18_k1_h7/core
> Do I have to pick one of these now?  Does anyone know which one corresponds
> to "regular" E.coli or the default one that used to be loaded?

Yes, you need to pick one - the escherichia_shigella_collection core 
contains a set of genomes in one db (this is to allow us to handle large 
numbers of genomes efficiently without having to deal with hundreds of 
databases). This has always been the case for all of our bacterial 
genomes and there has never been one definitive E. coli genome with the 
alias E. coli. I suspect that you may have inadvertently been picking up 
the first genome in the set (E. coli K12/MG155 which happens to be often 
used as the reference) by some fluke of the Registry code (which maybe 
has now changed), but it has never been intended to work this way. I 
suggest you either pick the genome you want from the list above, or use 
e_coli_k12 if you want the one mentioned above.

Hope this helps!


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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