[ensembl-dev] Translations

[Sam Seaver]

Dear Arnaud,

Apparently these embedded stop codons were found in a few sequences in
O. sativa and V. vinifera.  There was a miscommunication and by
"ignored", my colleague actually meant '*'.

However, your email provokes another question, how do you define
whether a stop codon actually belongs to another amino acid such as
Selenocystein.  Is this a case where, for the species, every instance
of TGA is known to belong to Selenocystein?

Thanks
Sam

On Thu, Oct 4, 2012 at 8:50 AM, Arnaud Kerhornou <arnaud at ebi.ac.uk> wrote:
> 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
>>
>



-- 
Postdoctoral Fellow
Mathematics and Computer Science Division
Argonne National Laboratory
9700 S. Cass Avenue
Argonne, IL 60439

http://www.linkedin.com/pub/sam-seaver/0/412/168
samseaver at gmail.com
(773) 796-7144

"We shall not cease from exploration
And the end of all our exploring
Will be to arrive where we started
And know the place for the first time."
   --T. S. Eliot