[ensembl-dev] Search in Variation Database

Will McLaren wm2 at ebi.ac.uk
Mon Jul 23 12:57:13 BST 2012


Sorry, that second coordinate should have been 57235280 as in your example.

Will

On 23 July 2012 12:56, Will McLaren <wm2 at ebi.ac.uk> wrote:
> Hi Pauline,
>
> The variation_feature table has a column, seq_region_id, which is a
> foreign key to the seq_region table that stores the chromosome
> identities.
>
> So, your query should look something like:
>
> SELECT vf.* FROM variation_feature vf, seq_region s
> WHERE vf.seq_region_id = s.seq_region_id
> AND s.name = '3'
> AND vf.seq_region_end >= 57230943
> AND vf.seq_region_start <= 57230943;
>
> Hope this helps
>
> Will McLaren
> Ensembl Variation
>
> On 23 July 2012 12:48, Pauline Raballand <pauline.raballand at gmail.com> wrote:
>> Hi,
>> I have downloaded Variation Database on my computer and installed it on my
>> database. It's working fine.
>>
>> I have just one problem, i don't see how to find variations in specific
>> region.
>>
>> For example : I want all variations which are on the chromosom 3 and between
>> the positions 57230943 and 57235280.
>> I don't see any table where you can put regions and chromosom (in the table
>> variation_feature, you can set region but that's all).
>>
>> Thank you for your help.
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe):
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>




More information about the Dev mailing list