[ensembl-dev] mapping pfam domains to exons in ensembl release 62

[Magali]

Hi Anupam,

If you want to use the API, your main entry point will be the
translation object.

For a given translation, you can get all the protein domains
$translation->get_all_ProteinFeatures('Pfam');

Via the translation's transcript, you can also get exons and their
coordinates
my $transcript = $translation->transcript;
my @exons = @{ $transcript->get_all_Exons };
foreach my $exon (@exons) {
  print $exon->seq_region_start . "\t" . $exon->seq_region_end . "\t" .
$exon->seq_region_name . "\n";
}

>From there, you can map your regions to the exon/gene objects.

Protein domains are only available via a translation, so you will not be
able to fetch directly pfam domains, but you should be able to get all
the proteins and their domains, then loop through them to find the ones
you need.


Hopefully that will help you get started.
If not, please let us know.


Regards,
Magali

On 16/08/13 17:04, anupam sinha wrote:
> Dear all,
>
>            I have a couple of tasks to accomplish for which I need
> some help.
> 1) My first task is to map pfam domains to exon sequences in Homo sapiens.
>
> 2) I have predicted disordered regions on proteins sequences
> downloaded from ensembl. Now I want to map these regions back to the
> exons/genes. Can it be done using ensembl API?
>
> Can anyone help me out and give me a few pointers so that I could
> solve these problems?
>
> Thanks and Regards,
>
> Anupam
>
>
>
>
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