[Bioperl-l] BlastPlus Masker

Mark A. Jensen maj at fortinbras.us
Tue Mar 23 14:15:38 EDT 2010

Specifying 'dustmasker' for a nucleotide database is roughly the same as "filter : low complexity regions" and "mask : lookup table only", I believe.
(There is also a facility for creating masks based on lowercase residues in a mask data fasta file; the blast+ utility is 'convert2blastmask'. You can run this with the SABlastPlus factory. I'm not very familiar with it, but you should be able to take the output file from this utility and feed it in to a new factory as the '-mask_data' to get what you want. (If anyone has done this, a brief step-by-step would be appreciated.))

cheers MAJ
  ----- Original Message ----- 
  From: Nils Müller 
  To: Mark A. Jensen 
  Sent: Tuesday, March 23, 2010 12:42 PM
  Subject: Re: [Bioperl-l] BlastPlus Masker

  Many thanks,
  is it the same as showed on the ncbi blast page (Filtering and Masking- filter: Low complexity regions  and  mask:Mask for lookup table only or Mask lower case letters)?

  2010/3/23 Mark A. Jensen <maj at fortinbras.us>

    Hi Nils,
    You don't have to specify a mask_data file; the factory should
    make it for you; try simply

    $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
    -db_name => 'my_masked_db',
    -db_data => 'myseqs.fas',
    -masker => 'dustmasker',

    -create => 1);

    -mask_data is there so that pre-made masks can be
    applied separately, or so you can name the file that
    is produced and preserve it; this is an "advanced feature",
    I suppose--
    ----- Original Message ----- From: "Nils Müller" <nils.mueller0 at googlemail.com>
    To: <bioperl-l at lists.open-bio.org>
    Sent: Sunday, March 21, 2010 11:17 AM
    Subject: [Bioperl-l] BlastPlus Masker

      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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