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


       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


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

        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*
        Function: Loads up (like use) a module at run time on demand