[ensembl-dev] Fwd: Queries regarding API

[Taruna Kewalya]

Hello
Thank you for your help regarding exons details but what I am confused
about is the position of exons in a FASTA sequence of a particular
protein.This is the link I am working over for my research
http://beta.rest.ensembl.org/feature/id/ENSG00000146648?feature=exon;content-type=application/json
from
Rest API 1.3.2 Please let me know how to refer start and end coordinates
with the FASTA sequence and get the exact position of exons with their
positions of amino acids in a protein sequence.
Thanking you


On Mon, Jun 24, 2013 at 6:43 PM, Emily Pritchard <emily at ebi.ac.uk> wrote:

>  Hi Taruna
>
> The REST link you've used asks for all the exons in a gene. The script
> returns these in a per-transcript manner, which means that some exons will
> appear more than once as they appear in more than one transcript.
>
> Let's take a look at the first line of the output:
>
> {"ID":"ENSE00001633131","feature_type":"exon","Parent":"ENST00000455089","ensembl_phase":"-1","end":55087058,"seq_region_name":"7","ensembl_end_phase":"1","strand":1,"constitutive":"0","rank":"1","start":55086714},
>
> This firstly gives me the exon ID, then tells me that it is an exon. The
> parent is the ID of the transcript that this exon is found in. The start
> and end coordinates refer to the genomic position of the exon, with the
> seq_region_name referring to the chromosome number, and strand indicating
> if it's on the positive (1) or negative (-1) strand. The phases refer to
> the position of the start and end of the exon in the codons. The rank is
> the position of the exon in the transcript.
>
> These are complete exons of the cDNA. Some of the them will include the
> UTRs of the transcripts and some will be of non-coding transcripts.
>
> Hope this helps
>
> Emily
> Ensembl helpdesk
>
>
> On 24/06/2013 13:20, Taruna Kewalya wrote:
>
>
>
> ---------- Forwarded message ----------
> From: Taruna Kewalya <kewalyataruna at gmail.com>
> Date: Thu, Jun 20, 2013 at 11:33 AM
> Subject: Queries regarding API
> To: dev at ensembl.org, ktaylor at ebi.ac.uk
>
>
> Hello
> I am Taruna Kewalya, student of Bioinformatics doing a research work on
> gene and transcript. Thank you for your reply it helped me in finding the
> details properly but now I am stuck with a new problem. I have downloaded
> the Rest API 1.3.2 link
> http://beta.rest.ensembl.org/feature/id/ENSG00000146648?feature=exon;content-type=application/json
>
> this shares a common parent id. So please let me know what is it relating
> to? The transcript belongs to cdna or cds or genomic and please let me know
> what this parent id refers to? And please also let me know how to
> understand the starting and ending position of exons in a Fasta sequence.
> Thanking you
>
>
>
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> --
> Dr Emily Pritchard
> Ensembl Outreach Officer
>
> EMBL - European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge
> CB10 1SD
> UK
>
>
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