Provided by: libbio-perl-run-perl_1.7.2-4_all bug


       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)