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://github.com/bioperl/bioperl-live/issues

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