Ensembl Core DB question (mapping amino acid region to genomic coordinates)
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5.8 years ago
djevrem • 0

I am using the Ensembl Core DB (described in http://uswest.ensembl.org/info/docs/api/core/core_schema.html) to query it emulating some of the Ensembl REST API functionality. Using the Ensembl protein ID and the amino acid range, as in the example:

 

http://grch37.rest.ensembl.org/map/translation/ENSP00000439902/3052..3190?content-type=application/json

will retrieve the mapping of the range 3052..3190 to the genomic coordinates in a JSON response. I am interested how is this implemented in the backend and using the Core DB schema with the three given parameters (ENSP00000439902, 3052,3190) how can I obtain the mapping data by SQL querying and which tables in the schema contain this information.

 

Thanks!

Ensembl protein domain mapping • 1.3k views
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The core database schema is here.
I suggest you contact the developers via the helpdesk for questions related to the backend.
In case you also had sequence retrieval in mind: "Also note that direct MySQL queries on the database are not suited to retrieve sequences; to retrieve sequences please use the Perl API."

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