Promoter sequence

[simonandrews]

Ok for biomart,

But I do not see where is the option for the promoter attribute ?

If you skip the filtering step all together (so you get information on all genes), and then select "Attributes". From there you can select "Sequences" from the radio button at the top, you can then select "Flank (Transcript)", and then you can specify how far back from the TSS you want your promoter sequence to extend.

[NicoBxl]

Ok for biomart,

But I do not see where is the option for the promoter attribute ?

[simonandrews]

Just to add to the list - I'd normally use BioMart to extract this kind of data.

http://www.ensembl.org/biomart/martview/

[ttnguyen]

Galaxy should be another option. You can get data from various servers.

http://main.g2.bx.psu.edu/

[mobdjek]

Hi Nico

Try http://rsat.ulb.ac.be/rsat/, alot of differenet tools there.
I think there is a tool called something like "retrieve ensembl seq." where you can define the regions you wish to retrieve. Also Bos Taurus


All the best
Morten

[NicoBxl]

Hi,

Where can I find the promoter sequence of all the gene of an organism (in this case Bos Taurus) ?

Thanks,

N.