[ensembl-dev] MySql Database

[Magali]

Hi Sunita,

The genomic sequence of the assembly is stored in the dna table, only in
the core database.
Generally though, features are stored on chromosomes, which themselves
are assembled from the various bits of genomic sequence stored in the
dna table.

We do not recommend querying the database directly to retrieve sequences.
We provide a number of tools to do so in an easier fashion.

If you are familiar with perl programming, you can use our perl API.
http://www.ensembl.org/info/docs/Doxygen/core-api/index.html

The sequences can also be downloaded via our ftp site
http://www.ensembl.org/info/data/ftp/index.html

Various endpoints can be retrieved using our new rest service
http://beta.rest.ensembl.org/

Or you can use our biomart server
http://www.ensembl.org/biomart/martview/07e32c2046773639dad947c91ff9ef7a


Hope that helps,
Magali


On 04/03/13 17:34, Koul, Sunita wrote:
>
> Hi,
>
> I  have locally setup the  mysql databases for Homo Sapiens
>
> Here are the different schemas I have
>
>  
>
> homo_sapiens_core_69_37
>
> homo_sapiens_cdna_69_37
>
> homo_sapiens_coreexpressionatlas_69_37
>
> ....
>
>  
>
> I am trying to figure out where the actual sequences are stored .
>
> For e.g if I am interested in a genomic sequence of "EGFR" gene how do
> I get it from these tables
>
>  
>
> Thanks
>
> Sunita
>
>
>
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