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Bio::Tools::Run::GenscUser)Contributed Perl DocumenBio::Tools::Run::Genscan(3)

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 v5.24.1			  2017-07-08	   Bio::Tools::Run::Genscan(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Bala | APPENDIX

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