Hi Rayna,

Did you check the bacteria ensembl BioMart?

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
......

You'll notice there are a few E. Coli strains in there, you can select one
as follows:

> mart=useMart("bacterial_mart_5",dataset="esc_30585_gene")
Checking attributes ... ok
Checking filters ... ok

To see what kind of data is available do:

> listAttributes(mart)
> listFilters(mart)

And then do your query with getBM

Hope this helps,
Steffen




On Fri, Aug 27, 2010 at 11:05 AM, Rayna <rayna.st@gmail.com> wrote:

> Dear all,
>
> I'm very new to R and BioConductor, but I somehow managed to deal with my
> ChIP-chip data (normalization and quality controls). The platform is
> Nimblegen ChIP for E. coli K12.
> My current problem is that I don't find a way to map my putative peaks to
> the genome. I tried using biomaRt but its Mart ensembl only allows to
> access
> the eukaryotic genomes. Given that there is an entry for E. coli in
> Ensembl,
> but it is not taken into account by biomaRt, I don't know how to do this
> mapping.
>
> Do you have any ideas?
>
> Thanks a lot in advance!
>
> Best,
> 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
>
>
>
> What happens when you've worked too long in the lab :
> *You wonder what absolute alcohol tastes like with orange juice.
> *Warning labels invoke curiosity rather than caution.
> *The Christmas nightout reveals scientists can't dance, although a formula
> for the movement of hands and feet combined with beats per min is found
> scrawled on a napkin by a waiter the next day.
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>
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