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

[Kieron Taylor]

Dear Matiss,

The jump in coordinates is caused by the intron between the exons involved in this protein sequence.

http://grch37.ensembl.org/Homo_sapiens/Transcript/Exons?g=ENSG00000166147;r=15:48408306-48645849;t=ENST00000316623

The link shows the splicing pattern, and why there would be a jump in coordinates. The grey sections do not contribute directly to the final protein sequence. Biology is messy!

Regards,

Kieron


Kieron Taylor PhD.
Ensembl Developer

EMBL, European Bioinformatics Institute






> On 5 Jul 2016, at 16:32, Matiss Ozols <matiss.ozols at manchester.ac.uk> wrote:
> 
> 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 _______________________________________________
>> Dev mailing list    Dev at ensembl.org
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> 
> 
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