- AUTHOR - Sendu Bala
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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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