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 - <span style="background:none repeat scroll 0% 0% yellow" class="J-JK9eJ-PJVNOc">preferably</span>
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 <span style="background:none repeat scroll 0% 0% yellow" class="J-JK9eJ-PJVNOc">discrepancies</span> large-<span style="background:none repeat scroll 0% 0% yellow" class="J-JK9eJ-PJVNOc">scale</span> sequence substitutions may be used but at least within <span style="background:none repeat scroll 0% 0% yellow" class="J-JK9eJ-PJVNOc">EG</span> <span style="background:none repeat scroll 0% 0% yellow" class="J-JK9eJ-PJVNOc">Metazoa</span>
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 <span style="background:none repeat scroll 0% 0% yellow" class="J-JK9eJ-PJVNOc">chado</span> imports where 'corrected' sequences are generally only stored at the peptide level we are a bit more conservative). <br>
<br>
<span style="background:none repeat scroll 0% 0% yellow" class="J-JK9eJ-PJVNOc">HTH</span><br>
<br>
<span style="background:none repeat scroll 0% 0% yellow" class="J-JK9eJ-PJVNOc">dan</span>.<br clear="all">Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)<br>-------------------------------------------------------------------------------------<br>
<a href="mailto:dsth@cantab.net">dsth@cantab.net</a><br><a href="mailto:dsth@cpan.org">dsth@cpan.org</a><br>
<br>
<br>
<br><br><div class="gmail_quote">2012/10/4 Sam <span style="background:none repeat scroll 0% 0% yellow" class="J-JK9eJ-PJVNOc">Seaver</span> <span dir="ltr"><<a href="mailto:samseaver@gmail.com" target="_blank"><span style="background:none repeat scroll 0% 0% yellow" class="J-JK9eJ-PJVNOc">samseaver</span>@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear ensembl-dev,<br>
<br>
A colleague has discovered that in a few of the plant genomes, the<br>
underlying DNA sequence of a CDS may have some embedded stop codons.<br>
He subsequently found that the resulting translation, as performed by<br>
Ensembl, ignores these completely.<br>
<br>
We were wondering what, if any, other problems are encountered when<br>
translating plant genes, and what the Ensembl translation code does to<br>
address these?<br>
<br>
Thanks<br>
Sam<br>
<br>
--<br>
Postdoctoral Fellow<br>
Mathematics and Computer Science Division<br>
Argonne National Laboratory<br>
9700 S. Cass Avenue<br>
Argonne, IL 60439<br>
<br>
<a href="http://www.linkedin.com/pub/sam-seaver/0/412/168" target="_blank">http://www.linkedin.com/pub/sam-seaver/0/412/168</a><br>
<a href="mailto:samseaver@gmail.com">samseaver@gmail.com</a><br>
<a href="tel:%28773%29%20796-7144" value="+17737967144">(773) 796-7144</a><br>
<br>
"We shall not cease from exploration<br>
And the end of all our exploring<br>
Will be to arrive where we started<br>
And know the place for the first time."<br>
--T. S. Eliot<br>
<br>
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<br>
</blockquote></div><br>