[ensembl-dev] Converting cDNA position to genomic position!

Will McLaren wm2 at ebi.ac.uk
Thu Nov 15 10:59:56 GMT 2012

Hello Oyediran,

You will need to use a TranscriptMapper object;

The method you should use is cdna2genomic. Note that this returns an array
of coordinate objects; this is useful to know if, for example, your
coordinates only partially overlap the transcript.

Here's a bit of code to get you started:

my $reg = 'Bio::EnsEMBL::Registry';
$reg->load_registry_from_db(-host => 'ensembldb.ensembl.org',-user =>

my $ta = $reg->get_adaptor('human','core','transcript');

my $t = $ta->fetch_by_stable_id('ENST00000373968');

my $mapper = Bio::EnsEMBL::TranscriptMapper->new($t);

@coords = $trmapper->cdna2genomic( 123, 554 );


Will McLaren
Ensembl Variation

On 15 November 2012 10:45, Oyediran Akinrinade <
oyediran.akinrinade at helsinki.fi> wrote:

> Hello,
> I have a list of ensembl transcripts IDs with their corresponding cDNA
> positions and I will like to get their genomic positions using the
> ensembl API. I have no experience with perl although I have
> installed ensembl-api on my mac computer. There are about 6000 IDs
> that I will like to get their genomic cordinates/positions, and
> web-based queries will not be the best solution. To this end, I
> write to request for your assistance.
> Looking forward to hearing from you soonest.
> Thanks,
> -Oyediran
> ______________________________**_________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/**mailman/listinfo/dev<http://lists.ensembl.org/mailman/listinfo/dev>
> Ensembl Blog: http://www.ensembl.info/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20121115/843025e2/attachment.html>

More information about the Dev mailing list