[Bioperl-l] low complexity filter in RemoteBlast

[Wiepert, Mathieu]

> Hi,
> does anyone know how to remove the low complexity filter while using
> RemoteBlast?
> my guess was:
> $RemoteBlast::HEADER{'FILTER'}='0';

Hmmm, good question.  The default header has the filter set to 'L'.  The URL API docs say that valid values are L, R, and m, otherwise not set.  I think you need to null out the Filter element if you want no filter (oddly enough the BLAST website seems momentarily down, so I can't test this)

delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'}; 

As an aside, I mimicked the Short Nearly exact protein matches this way.

my $factory = Bio::Tools::Run::RemoteBlast->new();
$Bio::Tools::Run::RemoteBlast::HEADER{'PROGRAM'} = 'blastp';
$Bio::Tools::Run::RemoteBlast::HEADER{'DATABASE'} = 'nr';
$Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '200000';
$Bio::Tools::Run::RemoteBlast::HEADER{'MATRIX_NAME'} = 'PAM30';
$Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '9 1';
$Bio::Tools::Run::RemoteBlast::HEADER{'WORD_SIZE'} = '2';
$Bio::Tools::Run::RemoteBlast::HEADER{'NCBI_GI'} = 'on';
$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]';
#Have to request the blast with the right amount of alignments, 
$Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENTS'} = '1000';
$Bio::Tools::Run::RemoteBlast::HEADER{'DESCRIPTIONS'} = '1000';
#and then retrieve it that way as well
$Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'ALIGNMENTS'} = '1000';
$Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'DESCRIPTIONS'} = '1000';
$Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'FORMAT_TYPE'} = 'Text';

my $r = $factory->submit_blast($inseqfile);

Let me know if that doesn't work,

-Mat