[Bioperl-l] Bio::DB::Query::GenBank retrieves fewer sequences than Webbrowser query

Paulo Almeida paulo.david at netvisao.pt
Tue Mar 23 17:06:19 EST 2004

I think you need to escape the brackets in Organism. Try replacing your 
query line with this:

(-query   =>'Mus\[Organism\] AND exon NOT mRNA NOT cDNA',   

Hope it works,
-Paulo Almeida

Jürgen Schmitz wrote:

The following query  retrieves less than a hundred sequences, much less 
than I get via Entrez:

my $query = Bio::DB::Query::GenBank->new
        (-query   =>'Mus[Organism] AND exon NOT mRNA NOT cDNA',
         -db      => 'nucleotide');
$seqio = $gb->get_Stream_by_query($query);
while( my $seq =  $seqio->next_seq ) {...}

but entering "Mus[Organism] AND exon NOT mRNA NOT cDNA" at
retrieves more than 5000 sequences.

What could be the problem ?
There are no error messages printed to STDERR.
I'm using Bioperl 1.4, Perl v5.8.1-RC3 on a MAC (OSX)

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