[ensembl-dev] Vertrna database

[Bronwen Aken]

Hi Alex,

The Vertebrate RNA (vertrna) database consists of the vertebrate mRNA sequence set in the European Nucleotide Archive (formerly EMBL).

We don't create the database ourselves; it is done for us by a Sanger bioinformatics team.

To download all vertebrate mRNAs from ENA you'll need to note the heirarchy of data storage in taxonomic divisions:
http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_2

I think it goes something like:
HUM = all human sequences
MUS = all mouse sequences
ROD = all non-mouse rodent sequences
MAM = all mammal sequences not in HUM, MUS or ROD
VRT = all vertebrate sequences not found in HUM, MUS, ROD or MAM

So, to get all vertebrate mRNA sequences I think you will need to modify your query to also fetch the HUM, MUS, ROD and MAM groups.

Also, you may need to specify which data classes you use. mRNAs may be found in HTC, STD, PAT.
http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_1

Cheers,
Bronwen


On 7 Oct 2010, at 18:11, Alex Humberto Di Genova Bravo wrote:

> Hi all:
> How I can get (download)  the Vertrna database?, My first approuch was using the following stament in the SRS website
> "[embl-mol:mRNA]&[embl-div:VRT]" but I get a total of 8786993 entries is this correct?.
> thank in advance
> 
> Alex Di Génova.
> Ingeniero en Bioinformatica.
> Laboratorio de Bioinformatica y Matemática del Genoma.
> Centro de Modelamiento Matemático.
> Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile.
> Avenida Blanco Encalada 2120, Piso 6.
> 
> 
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
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