NAME

       Bio::Tools::Run::Genscan - Object for identifying genes in a given sequence given a
       matrix(for appropriate organisms).

SYNOPSIS

         # Build a Genscan factory
         my $param = ('MATRIX'=>HumanIso.smat);
         my  $factory = Bio::Tools::Run::Genscan->new($param);

         # Pass the factory a Bio::Seq object
         #@genes is an array of Bio::Tools::Predictions::Gene objects
         my @genes = $factory->run($seq);

DESCRIPTION

       Genscan is a gene identifying program developed by Christopher Burge
       http://genes.mit.edu/burgelab/

       By default it looks for an executable called genscan and data/parameter files in the
       directory specified by the GENSCANDIR environmental variable.

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
        Args    :

   predict_genes()
           Title   :   predict_genes()
           Usage   :   DEPRECATED: use $obj->run($seq) instead
           Function:   Runs genscan and creates an array of Genes
           Returns :   An array of Bio::Tools::Prediction::Gene objects
           Args    :   A Bio::PrimarySeqI

   run
           Title   :   run
           Usage   :   $obj->run($seq)
           Function:   Runs genscan and creates an array of Genes
           Returns :   An array of Bio::Tools::Prediction::Gene objects
           Args    :   A Bio::PrimarySeqI

   _run
           Title   :   _run
           Usage   :   $obj->_run()
           Function:   Internal(not to be used directly)
           Returns :   An array of Bio::Tools::Prediction::Gene objects
           Args    :

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

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