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

[Man Chun John MA]

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) 
> 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 
> <mailto: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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