Provided by: libbio-perl-perl_1.6.901-2_all bug

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:

         https://redmine.open-bio.org/projects/bioperl/

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