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Hi Anupam,<br>
<br>
If you want to use the API, your main entry point will be the
translation object.<br>
<br>
For a given translation, you can get all the protein domains<br>
$translation->get_all_ProteinFeatures('Pfam');<br>
<br>
Via the translation's transcript, you can also get exons and their
coordinates<br>
my $transcript = $translation->transcript;<br>
my @exons = @{ $transcript->get_all_Exons };<br>
foreach my $exon (@exons) {<br>
print $exon->seq_region_start . "\t" . $exon->seq_region_end
. "\t" . $exon->seq_region_name . "\n";<br>
}<br>
<br>
From there, you can map your regions to the exon/gene objects.<br>
<br>
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.<br>
<br>
<br>
Hopefully that will help you get started.<br>
If not, please let us know.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 16/08/13 17:04, anupam sinha wrote:<br>
</div>
<blockquote
cite="mid:CAPPk2AhqHP=bU-8Xjt-y9Pq6C5bRARKfyDwQMsywfYcznzRqxw@mail.gmail.com"
type="cite">
<div dir="ltr">Dear all,
<div><br>
</div>
<div> I have a couple of tasks to accomplish for which
I need some help.</div>
<div>1) My first task is to map pfam domains to exon sequences
in Homo sapiens.</div>
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>Can anyone help me out and give me a few pointers so that I
could solve these problems?</div>
<div><br>
</div>
<div>Thanks and Regards,</div>
<div><br>
</div>
<div>Anupam<br clear="all">
<div><br>
</div>
<br>
</div>
</div>
<br>
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<br>
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</blockquote>
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