[ensembl-dev] From Exon coords to AA coords

[jmrodriguez]

Thanks Kieron. I will try with some of the ways you told me.

J

On 1/8/13 12:56 PM, Kieron Taylor wrote:
> 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.
>>
>>
>> -- 
>> *********************************************
>> Jose Manuel Rodriguez Carrasco
>> e-mail: jmrodriguez at cnio.es
>> Tlfn:    (+34) 91 732 80 00 ext: 3061
>>
>> Structural Biology and BioComputing Programme
>> Spanish National Cancer Center (CNIO)
>> Spanish National Bioinformatics Institute (INB) - http://www.inab.org -
>>
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-- 
*********************************************
Jose Manuel Rodriguez Carrasco
e-mail: jmrodriguez at cnio.es
Tlfn:    (+34) 91 732 80 00 ext: 3061

Structural Biology and BioComputing Programme
Spanish National Cancer Center (CNIO)
Spanish National Bioinformatics Institute (INB) - http://www.inab.org -

Address: C/ Melchor Fernandez Almagro 3, Madrid (Spain) ZipCode: 28029


**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.