[ensembl-dev] Could not retrieve the sequence of a gene

[Andy Yates]

Hi Jing,

I would urge caution performing this kind of operation. Ensembl stores DNA data on the lowest level of non-redundant sequence and then assembles higher levels of sequence regions, such as chromosomes and supercontigs, from these non-redundant blocks of data. There are enough pitfalls & edge cases involved which can easily trip you up. I would urge you to use the Perl API which is aware of every oddity of how we store our DNA data.

All the best,

Andy

---
Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 13 Jan 2012, at 07:10, jtang at mappi.helsinki.fi wrote:

> Hi,
> I tried to retrieve the actual sequence of the gene BRCA1 using SQL as:
> 
> 
> use homo_sapiens_core_65_37;
> select seq_region_id
> from xref
> join gene on xref_id=display_xref_id
> join seq_region using (seq_region_id)
> where display_label="BRCA1";
> 
> And the output is seq_region_id=27509, then retrieve with the id as:
> 
> select * from dna where seq_region_id=27509
> 
> But it returns empty result.
> 
> 
> Is there something wrong with my query?
> 
> Thanks!
> 
> Best,
> Jing
> 
> 
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