[Bioperl-l] retrieve ensembl sequence using bioperl

Mark Johnson johnsonm at gmail.com
Thu Jul 24 17:38:35 EDT 2008

On Thu, Jul 24, 2008 at 3:29 PM, Laurent Manchon
<lmanchon at univ-montp2.fr> wrote:
> try this: ENSTRUP00000005947

That's an Ensembl Peptide ID.  As Chris pointed out (I missed the
reference to Ensembl at the top of your original message), Ensembl !=

This is what I end up with:

use Bio::Perl;

my $seq = get_sequence('embl', 'ENSTRUP00000005947');

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: EMBL stream with no ID. Not embl in my book
STACK: Error::throw
STACK: Bio::Root::Root::throw
STACK: Bio::SeqIO::embl::next_seq
STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
STACK: Bio::Perl::get_sequence /gsc/lib/perl5/site_perl/5.8.7/Bio/Perl.pm:507
STACK: -:3

The response to a GET to this URL


is 'No entries found.'

Which Bio::SeqIO::embl of course does not consider valid EMBL format.

You can query Ensembl via the Ensembl Perl API.  You can find
documentation for that here:


Here are a couple tutorials I found via a quick Google search

Good luck!

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