[ensembl-dev] GRCh37 Protein sequence has asterisks

Alessandro Vullo avullo at ebi.ac.uk
Mon Dec 4 17:44:40 GMT 2017

Hi Luke,

The problem is likely to depend on RefSeq differing from the reference.
Are you using VEP and then retrieving the sequence as annotated by it?

Quoting the relevant people (VEP):

"VEP uses BAMs to correct RefSeqs that differ from the reference, and 
without those the API can give incorrect translations.

This will hopefully be fixed in future when the SeqEdit objects that VEP 
creates from the BAMs are incorporated directly into the otherfeatures DB."

Hope that helps,


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