<div dir="ltr">We're happy to host the plugin, you can branch and then submit a pull request.<div><br></div><div>You may also host it in your own GitHub repo (or other content site) and we can link to it in the plugin config/registry (<a href="https://github.com/Ensembl/VEP_plugins/blob/release/84/plugin_config.txt">https://github.com/Ensembl/VEP_plugins/blob/release/84/plugin_config.txt</a>).</div><div><br></div><div>Just let us know what suits you best.</div><div><br></div><div>Regards</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 22 June 2016 at 12:50, Man Chun John MA <span dir="ltr"><<a href="mailto:manchunjohn-ma@uiowa.edu" target="_blank">manchunjohn-ma@uiowa.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Will,<br>
<br>
The fact is I'm using VEP, although I was originally thinking of
using PeptideSeq (thus the question of TVA::peptide and ultimately
TVA::codon), since fasta outputs are more convenient for
downstream applications.<br>
<br>
PeptideSeq only limits to non-frameshift while Downstream only
limits to frameshift. What I'm thinking is to combine the codes of
the two plugin to make an omnibus peptide prediction plugin, and I
probably can do that on my own. The problem is uploading it;
should I branch off VEP/plugins from github or in some other way?<br>
<br>
Cheers,<span class=""><br>
<br>
Man Chun John Ma, PhD<br>
Postdoctoral Fellow<br>
Department of Lymphoma and Myeloma<br>
University of Texas MD Anderson Cancer Center<br>
Houston, Texas, USA<br>
<br></span><div><div class="h5">
On 6/22/2016 5:37 AM, Will McLaren wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>The peptide method does a somewhat limited translation; it
considers only the codon(s) covered by the reference
coordinates, expanded to the nearest complete codon(s). The
reason for this is to limit the length of the resultant alt
peptide sequence, since in theory this could run to hundreds
or even thousands of amino acids depending on the transcript
and the position of the frameshift.</div>
<div><br>
</div>
<div>An example:</div>
<div><br>
</div>
<div>ref codon: ATG, tranlsated to M</div>
<div>>> insert C between A and T</div>
<div>alt codon: ACTG</div>
<div>>> translate</div>
<div>alt peptide: TX (ACT -> T, G incomplete codon -> X)</div>
<div><br>
</div>
<div>The hgvs_protein method will give you a more informative
version of events, telling you where lies the new terminus
encountered in the shifted sequence. So for the same example
above you get p.Met268ThrfsTer57, so Met becomes Thr and the
new terminus is encountered 57 AAs downstream.</div>
<div><br>
</div>
<div>If you are a VEP user, the Downstream plugin (<a href="https://github.com/Ensembl/VEP_plugins/blob/release/84/Downstream.pm" target="_blank"></a><a href="https://github.com/Ensembl/VEP_plugins/blob/release/84/Downstream.pm" target="_blank">https://github.com/Ensembl/VEP_plugins/blob/release/84/Downstream.pm</a>)
will give you the full translated downstream sequence. You
could easily copy/paste the code from there into your own
code.</div>
<div><br>
</div>
<div>Hope that helps,</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 21 June 2016 at 13:12, Man Chun John
MA <span dir="ltr"><<a href="mailto:manchunjohn-ma@uiowa.edu" target="_blank">manchunjohn-ma@uiowa.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
Can you confirm that the peptide method in
Bio::EnsEMBL::Variation::TranscriptVariationAllele also
translates the peptide-level change caused by a frameshift
allele? I have noticed some similar methods in the Ensembl
API don't do that since it's computationally expensive, but
since method is Bio::Seq-based, I won't see it as a very
serious computational burden.<br>
<br>
By the way, I have changed my institution--is it appropriate
to keep on using the previous institution's email address in
this mailing list? My previous institution would keep this
email as a redirect indefinitely.<br>
<br>
Thanks for the answers in advance.<br>
<br>
Best regards,<br>
<br>
Man Chun John Ma, PhD<br>
Postdoctoral Fellow<br>
Department of Lymphoma and Myeloma<br>
University of Texas MD Anderson Cancer Center<br>
Houston, Texas, USA<br>
<br>
<br>
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