Convert mouse amino acid location to genomic location
I have amino acid positions for a number of mouse mutations, for example DNMT3a R878H. Is there a way to convert this to a genome coordinate such aschr12:12345?
The Ensembl Rest API seems to be capable of such a task, and when I make a call for a human change it works as shown here:
https://rest.ensembl.org/map/translation/ENSP00000288602/100..300?content-type=application/json
But when trying to change the gene to mouse the call no longer works.
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L. A. Liggett
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Thanks Pierre, I did have a look at this but it is unclear how to perform such an analysis for mouse. It looks like the Ensembl API might be able to do it as illustrated here, but how to switch from human to mouse is not clear to me.
Give VEP a shot
This doesn't seem to work for me either. I am trying to get the coordinates for the mouse
DNMT3a R878Hmutation in the question like this:But this will not return anything.
human, notmouse/mus_musculusThis works:
https://rest.ensembl.org/vep/mus_musculus/hgvs/ENSMUSP00000020991:p.Arg878His?content-type=application/json
"ENSMUSP00000020991" is actually protein id of "ENSMUSG00000020661".
Indeed. That's how I built the working URL from the "broken" URL
This works great! But how did you find the protein id instead of the gene id?