[Bioperl-l] BlastPlus Masker

Nils Müller nils.mueller0 at googlemail.com
Sun Mar 21 11:17:06 EDT 2010

Dear all,

I am confused in handeling with maskers in blastplus:
I have fasta seq. and want to run blast with a low complexity masker like

$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
  -db_name => 'my_masked_db',
  -db_data => 'myseqs.fas',
  -masker => 'dustmasker',
  -mask_data => 'maskseqs.fas',
  -create => 1);

Is myseqs.fas the same as maskseqs.fas??? I don't want to create a
maskfile , I only will run blast with a masked file??

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