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

Jürgen Schmitz jueschm at uni-muenster.de
Tue Mar 23 16:19:26 EST 2004


Hi All,

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)


Dr. Juergen Schmitz
Institute of Experimental Pathology (ZMBE)
University of Muenster
Von-Esmarch-Str. 56
D-48149 Muenster, Germany

Tel         +49  251  8352133
  Fax       +49  251  8358512


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