[ensembl-dev] querry about rest API, single nucleic coordinate for amino acid
Matiss Ozols
matiss.ozols at manchester.ac.uk
Tue Jul 5 16:24:15 BST 2016
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
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