[Bioperl-l] retrieve ensembl sequence using bioperl

Chris Fields cjfields at uiuc.edu
Thu Jul 24 15:55:27 EDT 2008


Note that you can't retrieve ***Ensembl*** seqs from bioperl, but you  
can get seqs from ***EMBL*** (two different beasts; the example code  
below is for EMBL retrieval).  You can use the ensembl perl API to  
retrieve seqs from ensembl, though.

chris

On Jul 24, 2008, at 2:45 PM, Mark Johnson wrote:

> On Thu, Jul 24, 2008 at 9:01 AM, Laurent Manchon
> <lmanchon at univ-montp2.fr> wrote:
>
>> #!/usr/bin/perl -w
>> use Bio::Perl;
>
> Ah.  Ye Olde Functional Interace.
>
>> if ($#ARGV < 0) {
>> print "Usage: $0 databaseID\n";
>> exit;
>> }
>> #database availables 'swiss','genbank','genpept','embl','refseq'
>> $seq_object = get_sequence('embl',$ARGV[0]);
>> write_sequence(">${ARGV[0]}.fasta",'fasta',$seq_object);
>
> Can you give us an example of an accession / identifier / whatever
> that does not work?  Are you sure your queries are valid EMBL
> accessions?  If you go here:
>
> http://www.ebi.ac.uk/ebisearch/
>
> and plug in your input, do you get any sequences returned?
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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