NAME

       Bio::Tools::Run::Seg - Object for identifying low complexity
         regions in a given protein seequence.

SYNOPSIS

         # Build a Seg factory
         # $paramfile is the full path to the seg binary file
         my @params = ('PROGRAM',$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);

DESCRIPTION

       Seg is a program which identifies low complexity regions in proteins.  It was developed by
       Wootton and Federhen at NCBI.

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 one of the Bioperl mailing lists.  Your
       participation is much appreciated.

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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       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.

   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:

         http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Bala

        Email savikalpa@fugu-sg.org

APPENDIX

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

   program_name
        Title   : program_name
        Usage   : $factory->program_name()
        Function: holds the program name
        Returns:  string
        Args    : None

   program_dir
        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

   new
        Title   : new
        Usage   : $rm->new(@params)
        Function: creates a new Seg factory
        Returns:  Bio::Tools::Run::Seg
        Args    :

   predict_protein_features
        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

   run
        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

   _input
        Title   :   _input
        Usage   :   obj->_input($seqFile)
        Function:   Internal (not to be used directly)
        Returns :
        Args    :

   _run
        Title   :   _run
        Usage   :   $obj->_run()
        Function:   Internal (not to be used directly)
        Returns :   An array of Bio::SeqFeature::Generic objects
        Args    :   None

   _writeSeqFile
        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