[ensembl-dev] Get genomic location for translatable cdna seq

Kieron Taylor ktaylor at ebi.ac.uk
Thu Feb 7 17:13:16 GMT 2013


Hi Abishek,

We need you to provide more specifics in order to determine what the 
difficulty is.

If you have Ensembl Exon objects, their coding_region_start() will 
inform you if the Exon does not code.

We can be of more assistance if you can tell us more or provide code 
samples. There are several ways to approach the task and we wouldn't 
want to recommend the most difficult for you!

Regards,

-- 
Kieron Taylor PhD.
Ensembl Core team
EBI


On 30/01/2013 15:15, Abhishek Niroula wrote:
> Hello,
>
> I am trying to get genomic co-ordinates for translatable portion of some
> human cdna sequences. I could succesfully extract the transcript start
> and end coordinates and also coordinates for each exon in a transcript.
> But, all the exons in a protein may not be translatable. I am stuck at
> this point.
> My goal is to check if a given genomic co-ordinate in a chromosome is
> located in protein coding (translatable region) of the chromosome.
>
> Thanks for your effort in advance.
>
> --
> Best Reagrds,
> Abhishek Niroula
>
>
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