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

[Matiss Ozols]

Sorry, its +1 not -1.

http://grch37.rest.ensembl.org/map/translation/ENSP00000325527/55..55?content-type=application/json

I think I resolved, It is broken down, and starts somewhere else after.

What is the reason of getting a result like this:

{"mappings":[{"assembly_name":"GRCh37","end":48936804,"seq_region_name":"15","gap":0,"strand":-1,"coord_system":"chromosome","rank":0,"start":48936803},{"assembly_name":"GRCh37","end":48905289,"seq_region_name":"15","gap":0,"strand":-1,"coord_system":"chromosome","rank":0,"start":48905289}]}


So the amino acid 55 would have nucleic acid coordinates 48936803, 48936804 and 48905289. Why is the last base far away?

Best regards,
Matiss



-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Matiss Ozols
Sent: 05 July 2016 16:24
To: Ensembl developers list
Subject: Re: [ensembl-dev] querry about rest API, single nucleic coordinate for amino acid

Dear Kieron,
Thank you for your response. The output was post-processed to get the nucleic acid coordinates only. And I still do get only 2 coordinates for http://grch37.rest.ensembl.org/map/translation/ENSP00000325527/53..53?content-type=application/json

54 was indicator for script, as we start to count from 0 amino acid.

Does anyone know the reason for having only 2 coordinates for this amino acid?

Best regards,
Matiss


-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Kieron Taylor
Sent: 16 June 2016 11:59
To: Ensembl developers list
Subject: Re: [ensembl-dev] querry about rest API, single nucleic coordinate for amino acid

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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