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bio::tools::run::tmhmm(3pm) [debian man page]

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

NAME

       Bio::Tools::Run::Tmhmm - Object for identifying transmembrane helixes
	 in a given protein seequence.

SYNOPSIS

	 # Build a Tmhmm  factory

	 # $paramfile is the full path to the seg binary file

	 my @params = ('PROGRAM',$paramfile);
	 my $factory = Bio::Tools::Run::Tmhmm->new($param);

	 # Pass the factory a Bio::Seq object
	 # @feats is an array of Bio::SeqFeature::Generic objects

	 my @feats = $factory->run($seq);

DESCRIPTION

       Tmhmm is a program for identifying transmembrane helices in proteins.

       You must have the environmental variable TMHMMDIR set to the base directory where tmhmm and it's associated data/option files reside (NOT
       the bin directory where the actual executable resides)

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

       head2 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, in this
		  case it is the tmhmm installation directory, not the location of
		  the executable.
	Returns:  string
	Args	:

   program_path
	Title	: program_path
	Usage	: my $path = $factory->program_path();
	Function: Builds path for executable
	Returns : string representing the full path to the exe
	Args	: none

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

   predict_protein_features
	Title	:   predict_protein_features()
	Usage	:   DEPRECATED Use $obj->run($seq) instead
	Function:   Runs Tmhmm and creates an array of featrues
	Returns :   An array of Bio::SeqFeature::Generic objects
	Args	:   A Bio::PrimarySeqI

   executable
	Title	: executable
	Usage	: my $exe = $tmhmm->executable('tmhmm');
	Function: Finds the full path to the 'tmhmm' executable
	Returns : string representing the full path to the exe
	Args	: [optional] name of executable to set path to
		  [optional] boolean flag whether or not warn when exe is not found

   run
	Title	:   run()
	Usage	:   $obj->run($seq)
	Function:   Runs Tmhmm 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	:

   _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::Tmhmm(3pm)

Check Out this Related Man Page

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)
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