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

[Will McLaren]

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> 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
>
>
> ---
> This email has been checked for viruses by Avast antivirus software.
> https://www.avast.com/antivirus
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160622/01c60322/attachment.html>