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Retrieving the corresponding Haplotype CDS from Ensembl

Given a Ensembl protein identifier and amino acid substitution such as ENSP00000242351:701Q>E,851T>I, how do I programmatically retrieve and download the coding sequence (CDS) with the largest observed count.

Screenshot of the corresponding Haplotype CDS

I need to do this for a batch of different proteins*haplotypes so would like to use the REST API.

gene ensembl protein haplotype
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updated by Emily Emily • written by Joseph Hughes Joseph Hughes

1 answer

This REST API endpoint gets the haplotypes per transcript. The protein haplotypes have the associated cds haplotypes stored as hexes, which you can link to the cds haplotypes.

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written by Emily Emily

So would this be taking the hex for the ENSP00000242351:701Q>E,851T>I in 'protein_haplotypes' and finding it as 'other_hex' in the 'cds_haplotypes'?

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written by Joseph Hughes Joseph Hughes

yes, this would be it. Or you can go the other way, and get the other_hex from the protein_haplotype and find the cds_haplotype it's the main hex for.

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written by Emily Emily

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