[Bioperl-l] accessing EMBL database

Mark A. Jensen maj at fortinbras.us
Thu Nov 19 08:10:07 EST 2009


Sandipan-- That id (CAB95729) returns "No entries" from EMBL.
I would agree that the error message is not really informative.
The module documentation warns:

      # remember that EMBL_ID does not equal GenBank_ID!
so I would check that.
MAJ
----- Original Message ----- 
From: "Sandipan Chowdhury" <sandipan.chowdhury at physiology.wisc.edu>
To: <bioperl-l at bioperl.org>
Sent: Thursday, November 19, 2009 1:49 AM
Subject: [Bioperl-l] accessing EMBL database


> Hi,
>
> I have 3 questions all related to the retreival of sequences from online 
> databases.
>
> (1) I have been trying to download a protein sequence from the EMBL database 
> and trying to write the sequence into a text file, as a string. I am using the 
> following code:
>
> use Bio::DB::EMBL;
> open b,">","s.txt";
> $em_obj = Bio::DB::EMBL->new;
>  $seq_obj = $em_obj->get_Seq_by_acc("CAB95729");
>  $s_str = $seq_obj->seq;
>  print b "$s_str\n";
> close b;
>
> The script is not working and gives the messege:
> "MSG: EMBL stream with no ID. Not embl in my book
> STACK: Error::throw
> STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm: 368
> STACK: Bio::SeqIO::embl::next_seq C:/Perl/site/lib/Bio\SeqIO\embl.pm: 203
> STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc 
> C:/Perl/site/lib/Bio/DB/WebDBSeqI.pm: 194
> STACK: trial2.pl"
>
> I am not sure what this means. A similar version of the script works for the 
> Swissprot, GenBank and RefSeq databases but not for the EMBL. What is the way 
> around this so that I can download the embl sequence?
>
> (2) Also, is there anyway I can download sequences from DDBJ (database of 
> Japan)?
>
> (3) Can GI numbers be used to retreive the sequences? If so then how?
>
> Answers to these questions would be greatly appreciated. I am very new to 
> Perl/Bioperl and am not really familiar with the advanced programming 
> features, so I would need to your help to find my way out of this situation.
>
> Many Thanks
> Sandipan
>
>
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> 



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