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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Mdust \- Perl extension for Mdust nucleotide filtering .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 2 \& use Bio::Tools::Run::Mdust; \& my $mdust = Bio::Tools::Run::Mdust\->new(); \& \& $mdust\->run($bio_seq_object); .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" Perl wrapper for the nucleic acid complexity filtering program \&\fBmdust\fR as available from \s-1TIGR\s0 via . Takes a Bio::SeqI or Bio::PrimarySeqI object of type \s-1DNA\s0 as input. .PP 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 \fImaskchar()\fR). .PP The mdust executable must be in a directory specified with either the \&\s-1PATH\s0 or \s-1MDUSTDIR\s0 environment variable. .SH "SEE ALSO" .IX Header "SEE ALSO" mdust, Bio::PrimarySeq, Bio::Seq::RichSeq, Bio::SeqFeature::Generic .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing Lists" .IX Subsection "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. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Support" .IX Subsection "Support" Please direct usage questions or support issues to the mailing list: .PP \&\fIbioperl\-l@bioperl.org\fR .PP rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. .SS "Reporting Bugs" .IX Subsection "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: .PP .Vb 1 \& http://redmine.open\-bio.org/projects/bioperl/ .Ve .SH "AUTHOR" .IX Header "AUTHOR" Donald Jackson (donald.jackson@bms.com) .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .SS "new" .IX Subsection "new" .Vb 10 \& 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 \*(AqExcluded\*(Aq, \& 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. .Ve .SS "run" .IX Subsection "run" .Vb 5 \& 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. .Ve .SS "target" .IX Subsection "target" .Vb 8 \& 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. .Ve .SS "maskchar" .IX Subsection "maskchar" .Vb 5 \& Title : maskchar \& Usage : $mdust\->maskchar(\*(AqN\*(Aq) \& Purpose : Set/get the character for masking low\-complexity regions \& Returns : True on success \& Args : Either N (default), X or L (lower case) .Ve