2010/8/27 Steffen Durinck <sdurinck@lbl.gov>

> Hi Rayna,
>

Hey,

Thanks for your quick response :)


>
> Did you check the bacteria ensembl BioMart?
>

Hum, I see my error: I directly did:
ensembl=useMart("ensembl")
Which is not the right Mart to use...


> If you do:
>
> > library(biomaRt)
> > listMarts()
>                      biomart
> 1                    ensembl
> 2                        snp
> 3        functional_genomics
> 4                       vega
> 5           bacterial_mart_5
>
> The 5th biomart is the bacteria BioMart of Ensembl. When you select that
> one and check which datasets it contains I get:
>
> > mart=useMart("bacterial_mart_5")
> > listDatasets(mart)
>            dataset                                          description
> version
> 1      str_57_gene          Streptococcus pneumoniae TIGR4 genes (EB 1)
> EB 1
> 2      esc_20_gene                  Escherichia coli Sakai genes (EB 1)
> EB 1
> 3   myc_25994_gene      Mycobacterium bovis Pasteur 1173P2 genes (EB 1)
> EB 1
> 4   sta_29522_gene               Staphylococcus aureus JH1 genes (EB 1)
> EB 1
> ......
>

I get the same stuff, #24 being E. coli K12 as you precise it in your next
mail.

So, all this seems perfect, I'll give feedback on querying bacterial BioMart
:)


Thanks a lot, nice evening.
Rayna
-- 
"Change l'ordre du monde plutôt que tes désirs."

Membre du CA de l'April - Promouvoir et défendre les logiciels libres (
www.april.org)

PhD Student
"Molecular Evolution and Bioinformatics"
Ludwig-Maximilians University (LMU) of Munich



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