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4 hours ago
Nikit
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I’m trying to use Ensembl’s REST API to programmatically retrieve a global amino acid alignment of orthologs for a given human protein.
For example, let’s say the gene of interest is ENSG00000169252. Through the Ensembl web interface, I can easily download a multiple sequence alignment of its orthologs (see attached screenshot).
However, I’d like to do this programmatically for hundreds of proteins.
Is there a way to obtain these ortholog alignments via the Ensembl REST API? I can't seem to figure out how to do it.
Looks like you can use something like
https://rest.ensembl.org/homology/id/human/ENSG00000169252?content-type=application/json
(following is for gene symbol)
https://rest.ensembl.org/homology/symbol/human/BRCA2?;type=orthologues;content-type=application/json;sequence=protein
You will need to parse JSON to get the info.