This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Ensembl API - Global Ortholog Alignments

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.

Exporting Ortholog Alignments thru Ensembl Web Interface:

alignment api ensembl orthologs

1 answer

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.

Log in to answer this question.