Christopher Fields > BioPerl > Bio::DB::TFBS



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Module Version: 1.006924   Source  


Bio::DB::TFBS - Access to a Transcription Factor Binding Site database


  use Bio::DB::TFBS;

  my $db = Bio::DB::TFBS->new(-source => 'transfac');
  my ($factor_id) = $db->get_factor_ids('PPAR-gamma1');
  my ($matrix_id) = $db->get_matrix_ids('PPAR-gamma1');

  # get a Bio::Map::TranscriptionFactor with all the positions of a given factor
  my $factor = $db->get_factor(-factor_id => $factor_id);

  # get a Bio::Map::GeneMap containing all the factors that bind near a given gene
  my $gene_map = $db->get_gene_map(-gene_name => 'AQP 7');

  # get a PSM (Bio::Matrix::PSM) of a given matrix
  my $psm = $db->get_matrix(-matrix_id => $matrix_id);

  # get the aligned sequences (Bio::SimpleAlign) that were used to build a given
  # matrix
  my $align = $db->get_alignment(-matrix_id => $matrix_id);

  # get a specific instance sequence (Bio::LocatableSeq)
  my $seq = $db->get_seq($id);


This is a front end module for access to a Transcription Factor Binding Site database.


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AUTHOR - Sendu Bala ^



Based on Bio::DB::Taxonomy by Jason Stajich




 Title   : new
 Usage   : my $obj = Bio::DB::TFBS->new(-source => 'transfac');
 Function: Builds a new Bio::DB::TFBS object.
 Returns : an instance of Bio::DB::TFBS
 Args    : -source => which database source: currently only 'transfac_pro'


 Title   : _load_tax_module
 Usage   : *INTERNAL Bio::DB::TFBS stuff*
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