[ensembl-dev] Translations

[Arnaud Kerhornou]

Dear Sam,

Could you give us the list of species where it is the case ?
There are some cases where the transcribed DNA sequence has stop codons 
but they're not real, and we have a mechanism in the Ensembl API to 
replace the stop codon by the right amino acid.

Typical case is for Selenocystein genes where an internal stop codon 
(TGA), which is replaced by a 'U' in the amino acid sequence.

In all cases, they should not be ignored. If we don't specify the 
correct amino acid behind a stop codon, it is not discarded and the 
amino acid sequence would hold an internal '*' character.

Arnaud

On 04/10/2012 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
>