I have a list of over a thousand protein accessions (from Ensembl Bacteria). I would like to download their gene locations, but obviously doing this through their website is unrealistic. I've been trying to figure this out in R using both the biomart package (it doesn't connect to the Bacteria database) and the ensembldb package, but I haven't been able to find an example of someone using it to connect to Ensembl Bacteria. Any guidance would be appreciated!
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biobaker •
You could use the Ensembl REST API lookup endpoints.
This is perfect, thank you! I was able to use the /lookup/id from R using the jsonlite package.
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