[Bioperl-l] accessing EMBL database

Hotz, Hans-Rudolf hrh at fmi.ch
Thu Nov 19 08:23:29 EST 2009


> 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?

"CAB95729" is a protein sequence, ie a translation of the CDS of

As far as I know, Bio::DB::EMBL is only designed to get EMBL entries, ie the
nucleotides sequence

> (2) Also, is there anyway I can download sequences from DDBJ (database of
> Japan)?

Unless, for network/speed reason, why do you want to download data from
DDBJ? It contains the same data as GenBank and EMBL. Those three databases
exchange their data on a daily basis.
> (3) Can GI numbers be used to retreive the sequences? If so then how?

Have you looked at Bio::DB::Eutilities ? See the 'HOWTOs'  page in the
Bioperl Wiki

Regards, Hans

> 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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