[ensembl-dev] Mysql_Translation strand

[Andy Yates]

Hi,

Firstly please do not use MySQL for the extraction of lengths; this is not well supported in anything apart from the Ensembl Perl API AFAIK. 

Coordinates given in the translation table are with respect to exon in question e.g. where seq_start equals 1 means translation starts at position 1 in the exon given in start_exon_id; seq_end equals 60 means finish at position 60 in the exon given in end_exon_id. These are given in the 5' to 3' ordering.

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 14 Sep 2012, at 10:19, enrico1970 at yahoo.com wrote:

> Hi there!
> I wish to retrieve the 5' and 3' length of each isoforms.
>  
> For this reason I am working on the Mysql table Translation of the core ensemble database:
>  
> http://www.ensembl.org/info/docs/api/core/core_schema.html#translation
> From the table description is unclear if the translation strand is forward or it is the same of the related transcript.
>  
> Thanks,
>  
> Enrico
> _______________________________________________
> 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/