[ensembl-dev] sequence of genomic features

[Jayaraman, Pushkala]

Thanks Andy!

-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Andy Yates
Sent: Friday, September 06, 2013 2:51 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] sequence of genomic features

Hi,

Ensembl holds DNA non-redundantly at the contig level. These are assembled into chromosome sequence on the fly using the API. We do not recommend reconstructing the chromosome yourself; it is non-trivial process. Instead you can get DNA sequences from:

* The Perl API
* Our FTP site (http://www.ensembl.org/info/data/ftp/index.html)
* Our REST API (http://beta.rest.ensembl.org/)
* BioMart (http://www.ensembl.org/biomart/martview)

Andy

------------
Andrew Yates - Ensembl Core Software Project Leader European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD
Tel: +44-(0)1223-492538
Fax: +44-(0)1223-494468
http://www.ensembl.org/

On 6 Sep 2013, at 00:13, "Jayaraman, Pushkala" <pjayaraman at mcw.edu> wrote:

> I am trying to retrieve sequence of a given genomic feature for eg. Retrieve sequence of gene "A2m"
>  
> I know that I can get the "seq_region_id" from the database for the 
> chromosome number and the coord_system_id is 2 But I cannot find the 
> sequence in the homo_sapiens_core_72_37.dna
>  
> Are we supposed to download the fasta sequences separately elsewhere?
> or am I missing a table?
>  
>  
> Thanks,
> Pushkala Jayaraman
> Programmer/Analyst - Rat Genome Database Human and Molecular Genetics 
> Center Medical College of Wisconsin
> 414-955-2229
> http://rgd.mcw.edu
>  
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