[ensembl-dev] querry about rest API, single nucleic coordinate for amino acid

Kieron Taylor ktaylor at ebi.ac.uk
Thu Jun 16 11:58:59 BST 2016


Dear Matiss,

Thank you for using our REST API. 

When I run your examples, I see the following.


http://grch37.rest.ensembl.org/map/translation/ENSP00000325527/54..54?content-type=application/json

{
  "mappings": [
    {
      "assembly_name": "GRCh37",
      "end": 48936807,
      "seq_region_name": "15",
      "gap": 0,
      "strand": -1,
      "coord_system": "chromosome",
      "rank": 0,
      "start": 48936805
    }
  ]
}


http://grch37.rest.ensembl.org/map/translation/ENSP00000325527/82..82?content-type=application/json;

{
  "mappings": [
    {
      "assembly_name": "GRCh37",
      "end": 48905210,
      "seq_region_name": "15",
      "gap": 0,
      "strand": -1,
      "coord_system": "chromosome",
      "rank": 0,
      "start": 48905208
    }
  ]
}

I don't understand how you have received a different output. Please provide more information to help us duplicate your issue, perhaps a gist of your client code.

Regards,

Kieron


Kieron Taylor PhD.
Ensembl Developer

EMBL, European Bioinformatics Institute






> On 16 Jun 2016, at 11:44, Matiss Ozols <matiss.ozols at manchester.ac.uk> wrote:
> 
> Dear Ensembl team,
> I have a query about mapping from protein coordinates to genomic coordinates:
> When I map each amino acid I usually expect to get 3 nucleic acid coordinates, however in some cases I get only 2 or 1 coordinates. What would be the reason for this?
>  
> I use python to do this and my code is following:
>  
> ext = "http:/grch37.rest.ensembl.org/map/translation/ENSP00000325527/82..82;
>  
> this gives me a result: [48905207] – why is it just one nucleic acid coordinate instead of 3?
>  
> In other case : ext = "http:/grch37.rest.ensembl.org/map/translation/ENSP00000325527/54..54; Gives me :[48936803| 48936804]
> ;
>  
> However most of the time it is 3 coordinates as I expect it to be.
>  
> Hope you can help,
> Best regards,
>  
>  
> Matiss Ozols (Beng),
> PhD researcher, School of Inflamation & Repair,
> University of Manchester
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