Mdust - Perl extension for Mdust nucleotide filtering


  use Bio::Tools::Run::Mdust;
  my $mdust = Bio::Tools::Run::Mdust->new();



Perl wrapper for the nucleic acid complexity filtering program mdust as available from TIGR via Takes a Bio::SeqI or Bio::PrimarySeqI object of type DNA as input.

If a Bio::Seq::RichSeqI is passed then the low-complexity regions will be added to the feature table of the target object as Bio::SeqFeature::Generic items with primary tag = 'Excluded' . Otherwise a new target object will be returned with low-complexity regions masked (by N's or other character as specified by maskchar()).

The mdust executable must be in a directory specified with either the PATH or MDUSTDIR environment variable.


mdust, Bio::PrimarySeq, Bio::Seq::RichSeq, Bio::SeqFeature::Generic


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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


  Title         : new
  Usage         : my $mdust = Bio::Tools::Run::Mdust->new( -target => $target_bioseq)
  Purpose       : Create a new mdust object
  Returns       : A Bio::Seq object
  Args          : target - Bio::Seq object for masking - alphabet MUST be DNA.
                  wsize - word size for masking (default = 3)
                  cutoff - cutoff score for masking (default = 28)
                  maskchar - character for replacing masked regions (default = N)
                  coords - boolean - indicate low-complexity regions as 
                           objects with primary tag 'Excluded', 
                           do not change sequence (default 0)
                  tmpdir - directory for storing temporary files
                  debug - boolean - toggle debugging output, 
                          do not remove temporary files
  Notes         : All of the arguments can also be get/set with their own accessors, such as:
                  my $wsize = $mdust->wsize();

                  When processing multiple sequences, call Bio::Tools::Run::Mdust->new() once 
                  then pass each sequence as an argument to the target() or run() methods.


  Title         : run
  Usage         : $mdust->run();
  Purpose       : Run mdust on the target sequence
  Args          : target (optional) - Bio::Seq object of alphabet DNA for masking
  Returns       : Bio::Seq object with masked sequence or low-complexity regions added to feature table.


  Title         : target
  Usage         : $mdust->target($bio_seq)
  Purpose       : Set/get the target (sequence to be filtered).  
  Returns       : Target Bio::Seq object
  Args          : Bio::SeqI or Bio::PrimarySeqI object using the DNA alphabet (optional)
  Note          : If coordinate parsing is selected ($mdust->coords = 1) then target
                  MUST be a Bio::Seq::RichSeqI object.  Passing a RichSeqI object automatically
                  turns on coordinate parsing.


  Title         : maskchar
  Usage         : $mdust->maskchar('N')
  Purpose       : Set/get the character for masking low-complexity regions
  Returns       : True on success
  Args          : Either N (default), X or L (lower case)