[ensembl-dev] Dev Digest, Vol 13, Issue 34

Steve Moss S.P.Moss at 2007.hull.ac.uk
Fri Jul 29 12:21:16 BST 2011

Hi Gonzalo,

I have done analyses on the UTRs before using this method and if I remember
correctly a start() and end() coordinates method isn't available for the 5'
and 3' UTRs. The way I did this was using the start and end coordinates of
the transcript and the start and end of the coding region respectively.
Obviously taking into account the strand!


my $cds_stt = $transcript->coding_region_start;
my $cds_end = $transcript->coding_region_end;

if ($transcript->strand == 1) {
     my $fputr_stt = $transcript->start;
     my $fputr_end = $cds_stt - 1;
else {
     my $fputr_stt = $transcript->end;
     my $fputr_end = $cds_end + 1;

Kindest regards,

Steve Moss

On 29 July 2011 12:00, <dev-request at ensembl.org> wrote:

> Message: 5
> Date: Thu, 28 Jul 2011 20:02:51 -0300
> From: Gonzalo Parra <gonza_parra at hotmail.com>
> Subject: [ensembl-dev] five_prime_utr
> To: <dev at ensembl.org>
> Message-ID: <BAY165-W374800E487E4B4266C57029D340 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
> Hello people, Im new with this.
> I need to obtains the limits of five_prime_utr region.
> I do print $transcript->five_prime_utr()->start."
> ".$transcript->five_prime_utr()->end."\n";Like a saw in some forums and I
> get this
> Can't locate object method "start" via package "Bio::Seq" at
> Ensemblapi_one_tr.pl line 41.
> Could you help me please?
> Thanks in advance

Kindest regards,

Steve Moss, BSc (Hons)
PhD Research Student
Evolutionary Biology Group
Department of Biological Sciences
University of Hull
Cottingham Road
Hull, HU6 7RX
Evolution site: http://goo.gl/7ZReN
site: http://goo.gl/LzGQo
Personal site: http://stevemoss.ath.cx/
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