[ensembl-dev] Translations

[Andy Yates]

Dear Sam,

Ensembl delegates the job of translating from CDS to protein to BioPerl. We also allow a codon table identifier to be set as a seq region attribute (according to those at http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) allowing people to use different codon tables (such as bacteria genomes). There are also other mechanisms in place where Ensembl can substitute amino acids to cope with a post-translation modification (such as Selenocysteine). 

Without specific examples it's hard to diagnose the cause of your issue. If you could send some examples thought I'm sure Ensembl Plants & Gramene would be interested in these cases (as would we if it showed up an issue with our code).

Regards,

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 4 Oct 2012, at 14:30, Sam Seaver wrote:

> Dear ensembl-dev,
> 
> A colleague has discovered that in a few of the plant genomes, the
> underlying DNA sequence of a CDS may have some embedded stop codons.
> He subsequently found that the resulting translation, as performed by
> Ensembl, ignores these completely.
> 
> We were wondering what, if any, other problems are encountered when
> translating plant genes, and what the Ensembl translation code does to
> address these?
> 
> Thanks
> Sam
> 
> -- 
> Postdoctoral Fellow
> Mathematics and Computer Science Division
> Argonne National Laboratory
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> 
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