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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::Seg 3pm"
.TH Bio::Tools::Run::Seg 3pm 2024-04-27 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH NAME
Bio::Tools::Run::Seg \- Object for identifying low complexity
  regions in a given protein seequence.
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 4
\&  # Build a Seg factory
\&  # $paramfile is the full path to the seg binary file
\&  my @params = (\*(AqPROGRAM\*(Aq,$paramfile);
\&  my $factory = Bio::Tools::Run::Seg\->new($param);
\&
\&  # Pass the factory a Bio::Seq object
\&  # @feats is an array of Bio::SeqFeature::Generic objects
\&  my @feats = $factory\->run($seq);
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
Seg is a program which identifies low complexity regions in proteins.
It was developed by Wootton and Federhen at NCBI.
.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 one
of the Bioperl mailing lists.  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
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 \- Bala"
.IX Header "AUTHOR - Bala"
.Vb 1
\& Email savikalpa@fugu\-sg.org
.Ve
.SH APPENDIX
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS program_name
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory\->program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS program_dir
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns : string, or undef if $SEGDIR not in ENV
\& Args    : None
.Ve
.SS new
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : $rm\->new(@params)
\& Function: creates a new Seg factory
\& Returns:  Bio::Tools::Run::Seg
\& Args    :
.Ve
.SS predict_protein_features
.IX Subsection "predict_protein_features"
.Vb 5
\& Title   :   predict_protein_features()
\& Usage   :   DEPRECATED Use $obj\->run($seq) instead
\& Function:   Runs Seg and creates an array of featrues
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :   A Bio::PrimarySeqI
.Ve
.SS run
.IX Subsection "run"
.Vb 5
\& Title   :   run
\& Usage   :   $obj\->run($seq)
\& Function:   Runs Seg and creates an array of featrues
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :   A Bio::PrimarySeqI
.Ve
.SS _input
.IX Subsection "_input"
.Vb 5
\& Title   :   _input
\& Usage   :   obj\->_input($seqFile)
\& Function:   Internal (not to be used directly)
\& Returns :
\& Args    :
.Ve
.SS _run
.IX Subsection "_run"
.Vb 5
\& Title   :   _run
\& Usage   :   $obj\->_run()
\& Function:   Internal (not to be used directly)
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :   None
.Ve
.SS _writeSeqFile
.IX Subsection "_writeSeqFile"
.Vb 5
\& Title   :   _writeSeqFile
\& Usage   :   obj\->_writeSeqFile($seq)
\& Function:   Internal (not to be used directly)
\& Returns :   string \- Fasta filename to which $seq was written
\& Args    :   Bio::Seq object
.Ve