[Bioperl-l] RemoteBlast VS Traditional Browser Blast

[facemann]

I have found the HEADER values and matched them but my scores still differ.  This is causing a bit of head scratching...
I have matched everything that I thought could cause a difference and a few that shouldn't make the slightest difference.
My HEADER code:
 
my @params = ( '-prog' => $prog,
         '-data' => $db,
         '-expect' => $e_val,
         '-readmethod' => 'SearchIO' );
my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
$Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENT_VIEW'} = 'Pairwise';
$Bio::Tools::Run::RemoteBlast::HEADER{'AUTO_FORMAT'} = 'Semiauto';
$Bio::Tools::Run::RemoteBlast::HEADER{'DATABASE'} = 'nr';
$Bio::Tools::Run::RemoteBlast::HEADER{'HITLIST_SIZE'} = '3';
$Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '10';
$Bio::Tools::Run::RemoteBlast::HEADER{'WORD_SIZE'} = '11';
$Bio::Tools::Run::RemoteBlast::HEADER{'FORMAT_OBJECT'} = 'Alignment';
$Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'plain';
# the following line locks up the query
#$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'all';
$Bio::Tools::Run::RemoteBlast::HEADER{'GET_SEQUENCE'} = 'on';
$Bio::Tools::Run::RemoteBlast::HEADER{'NCBI_GI'} = 'on';
$Bio::Tools::Run::RemoteBlast::HEADER{'PAGE'} = 'Nucleotides';
delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};

print $factory->header, "\n";



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