[ensembl-dev] From Exon coords to AA coords

[Kieron Taylor]

Dear Jose,

Normally the API tries to hide away the process of computing peptides, hence it is not easy for you to run it in reverse to get back to the orignal Exon. 

There are many ways to get there, some more convoluted than others. Our favourite is as follows:

i) Exon->seq_region_start  +  exon position of interest = genomic coordinates of your exon coordinate

ii) Project genomic coordinate to peptide coordinate using TranscriptMapper->genomic2pep
http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1TranscriptMapper.html


iii) Look up computed peptide coordinate in peptide you started with.

Note that genomic2pep typically works on more than one base, but it should be ok to restrict it to a single position of interest. Expect a single-membered list.

Hopefully that is enough to get you started.

Regards,

Kieron Taylor PhD.
Ensembl Core software developer

EMBL - European Bioinformatics Institute


On 8 Jan 2013, at 09:45, jmrodriguez wrote:

> Hello,
> 
> From Ensembl API, I am trying to obtain the AA Coords of a transcript-translation regarding to Exon coordinates.
> I am looking for a method of a class which retrieves that information but I don't find it.
> 
> Could anyone help me?
> 
> Bests Regards,
> Jose Manuel.
> 
> 
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