[ensembl-dev] 3' UTR Genomic coordinates from API

[Andy Yates]

Hi Afonso,

Sorry for such a long wait for this reply. UTR coordinates are not that easy to extract but I've put together a short script available from https://gist.github.com/1237394 how it's done for a number of example transcripts including those which lack a UTR. You need to take the CDNA coding start & end, convert these to genomic locations, take the transcript start/end and then do some strand detection to see which way you need to shift the coordinates.

Best regards,

Andy

On 22 Sep 2011, at 11:34, José Afonso Guerra Assunção wrote:

> Hi,
> 
> I'm trying to get the Ensembl API to give me all 3'UTRs in the Human
> genome, including their coordinates. It is straightforward to get the
> UTR sequences, but I can't figure out a way to get the UTR
> coordinates... what is the best way to do this?
> 
> Thanks!
> Afonso
> 
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Andrew Yates                   Ensembl Core Software Project Leader
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