debian man page for bio::tools::run::genscan

Bio::Tools::Run::Genscan(3pm)				User Contributed Perl Documentation			     Bio::Tools::Run::Genscan(3pm)

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    :

perl v5.12.3							    2011-06-18					     Bio::Tools::Run::Genscan(3pm)