[ensembl-dev] Translations

[Daniel Hughes]

I don't work on the plants but can tell you that it generally depends upon
the specific resources used to import the data. in a worst case scenario in
which the 'correct' sequence cannot be recovered they made be demoted to
something termed 'non_coding_cds' (still viewable but don't go into
comparative analysis etc.). however, we prefer to generate sequence edit
objects - preferably at the transcript level to allow for the
'modifications' to propagate up to the peptides too (these are applied in
the api after exon splicing). in cases in which there are severe
discrepancies large-scale sequence substitutions may be used but at least
within EG Metazoa we are increasingly using dynamic programming to generate
the parsimonious sequence of insertion/deletion/substitutions to reconcile
conflicts between genomic and transcript level evidence (though in the case
of chado imports where 'corrected' sequences are generally only stored at
the peptide level we are a bit more conservative).

HTH

dan.
Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org




2012/10/4 Sam Seaver <samseaver at gmail.com>

> 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
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