Bio::Map::TranscriptionFactor man page on Fedora

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Bio::Map::TranscriptioUsertContributed Perl DoBio::Map::TranscriptionFactor(3)

NAME
       Bio::Map::TranscriptionFactor - A transcription factor modelled as a
       mappable element

SYNOPSIS
	 use Bio::Map::TranscriptionFactor;
	 use Bio::Map::GeneMap;
	 use Bio::Map::Position;

	 # model a TF that binds 500bp upstream of the BRCA2 gene in humans and
	 # 250bp upstream of BRCA2 in mice
	 my $tf = Bio::Map::TranscriptionFactor->get(-universal_name => 'tf1');
	 my $map1 = Bio::Map::GeneMap->get(-universal_name => "BRCA2",
					   -species => "human");
	 my $map2 = Bio::Map::GeneMap->get(-universal_name => "BRCA2",
					   -species => "mouse");
	 Bio::Map::Position->new(-map => $map1,
				 -element => $tf,
				 -start => -500,
				 -length => 10);
	 Bio::Map::Position->new(-map => $map2,
				 -element => $tf,
				 -start => -250,
				 -length => 10);

	 # Find out where the transcription factor binds
	 foreach $pos ($tf->get_positions) {
	   print $tf->universal_name, " binds at position " $pos->value, " relative to ",
		 $pos->relative->description, " of gene ",
		 $pos->map->universal_name, " in species ", $pos->map->species, "\n";
	 }

DESCRIPTION
       A transcription factor modelled as a mappable element. It can have
       mulitple binding sites (positions) near multiple genes (maps).

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 the
       Bioperl mailing list.  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 of
       the bugs and their resolution. Bug reports can be submitted via the
       web:

	 http://bugzilla.open-bio.org/

AUTHOR - Sendu Bala
       Email bix@sendu.me.uk

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

   new
	Title	: new
	Usage	: my $tf = Bio::Map::TranscriptionFactor->new();
	Function: Builds a new Bio::Map::TranscriptionFactor object
	Returns : Bio::Map::TranscriptionFactor
	Args	: -universal_name => string name of the TF (in a form common to all
				     species that have the TF, but unique amongst
				     non-orthologous TFs), REQUIRED
		  -description	  => string, free text description of the TF

   get
	Title	: get
	Usage	: my $obj = Bio::Map::TranscriptionFactor->get();
	Function: Builds a new Bio::Map::TranscriptionFactor object (like new()), or
		  gets a pre-existing one that shares the same universal_name.
	Returns : Bio::Map::TranscriptionFactor
	Args	: -universal_name => string name of the TF (in a form common to all
				     species that have the TF, but unique amongst
				     non-orthologous TFs), REQUIRED
		  -description	  => string, free text description of the TF

   universal_name
	Title	: universal_name
	Usage	: my $name = $obj->universal_name
	Function: Get/Set TF name, corresponding to the name of the TF in a form shared
		  by orthologous versions of the TF in different species, but otherwise
		  unique.
	Returns : string
	Args	: none to get, OR string to set

   description
	Title	: description
	Usage	: my $desc = $obj->description
	Function: Get/Set a description of the TF.
	Returns : string
	Args	: none to get, OR string to set

perl v5.14.1			  2011-07-22  Bio::Map::TranscriptionFactor(3)
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