NAME

Mdust - Perl extension for Mdust nucleotide filtering

SYNOPSIS

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

  $mdust->run($bio_seq_object);

DESCRIPTION

Perl wrapper for the nucleic acid complexity filtering program mdust as available from TIGR via http://www.tigr.org/tdb/tgi/software/. Takes a Bio::PrimarySeq object of type DNA as input. Returns a Bio::Seq object with the low-complexity regions changed to Ns, or a Bio::Seq::RichSeq object with the low-complexity regions identified as a Bio::SeqFeature::Generic with primary tag = 'Excluded'.

This module uses the environment variable MDUSTDIR to find the mdust program. Set MDUSTDIR to the directory containing the mdust binary. For example, if mdust is installed as /usr/local/bin/mdust, set MDUSTDIR to /usr/local/bin.

SEE ALSO

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

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.open-bio.org/

AUTHOR

Donald Jackson (donald.jackson@bms.com)

APPENDIX

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

new

  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 
                           Bio::SeqFeature::Generic 
                           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
  Note          : All of the arguments can also be get/set with their own accessors, such as:
                  my $wsize = $mdust->wsize();

run

  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 (see 'new' for details)

target

  Title         : target
  Usage         : $mdust->target($bio_seq)
  Purpose       : Set/get the target (sequence to be filtered).  
  Returns       : Target Bio::Seq object
  Args          : Bio::Seq object using the DNA alphabet (optional)