[ensembl-dev] Some RefSeq transcripts seem broken

[João Eiras]

On 27 September 2016 at 14:26, Will McLaren <wm2 at ebi.ac.uk> wrote:
> Yes, my reply still stands.
>
> The protein sequence as stored in $tva->transcript_variation->_peptide is
> extracted from the protein sequence as constructed by the Ensembl API (from
> the imported RefSeq coords and the genomic sequence), *not* from the protein
> sequence as given in the RefSeq record. The reasons for this are explained
> in my initial reply.
>
> Unfortunately this is how our whole API is designed, and we are currently
> looking for better solutions at dealing with situations where the RefSeq
> sequence differs from the genome.
>
> Hopefully that makes more sense?
>

Ah, ok. So you understand that the problem exists and it will
hopefully be fixed in the future. That was the whole point for me to
ask about this anyway,

I got a bit confused because I thought when you meant "the protein
sequence as constructed by the Ensembl API"  you somehow referred to
VEP producing an mutated sequence.

Thank you very much for your time.