[ensembl-dev] Bio::EnsEMBL::Variation::TranscriptVariationAllele::peptide

Will McLaren wm2 at ebi.ac.uk
Wed Jun 22 12:58:17 BST 2016


We're happy to host the plugin, you can branch and then submit a pull
request.

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 (
https://github.com/Ensembl/VEP_plugins/blob/release/84/plugin_config.txt).

Just let us know what suits you best.

Regards

Will

On 22 June 2016 at 12:50, Man Chun John MA <manchunjohn-ma at uiowa.edu> wrote:

> Hi Will,
>
> 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.
>
> 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?
>
> Cheers,
>
> Man Chun John Ma, PhD
> Postdoctoral Fellow
> Department of Lymphoma and Myeloma
> University of Texas MD Anderson Cancer Center
> Houston, Texas, USA
>
> On 6/22/2016 5:37 AM, Will McLaren wrote:
>
> Hi,
>
> 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.
>
> An example:
>
> ref codon: ATG, tranlsated to M
> >> insert C between A and T
> alt codon: ACTG
> >> translate
> alt peptide: TX (ACT -> T, G incomplete codon -> X)
>
> 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.
>
> If you are a VEP user, the Downstream plugin (
> <https://github.com/Ensembl/VEP_plugins/blob/release/84/Downstream.pm>
> https://github.com/Ensembl/VEP_plugins/blob/release/84/Downstream.pm)
> will give you the full translated downstream sequence. You could easily
> copy/paste the code from there into your own code.
>
> Hope that helps,
>
> Will McLaren
> Ensembl Variation
>
>
>
> On 21 June 2016 at 13:12, Man Chun John MA <manchunjohn-ma at uiowa.edu>
> wrote:
>
>> Hi,
>>
>> 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.
>>
>> 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.
>>
>> Thanks for the answers in advance.
>>
>> Best regards,
>>
>> Man Chun John Ma, PhD
>> Postdoctoral Fellow
>> Department of Lymphoma and Myeloma
>> University of Texas MD Anderson Cancer Center
>> Houston, Texas, USA
>>
>>
>> ---
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>
>
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