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

NAME

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

SYNOPSIS

         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);

DESCRIPTION

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

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

CONTRIBUTORS

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

APPENDIX

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

   new
        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'

   _load_tax_module
        Title   : _load_tax_module
        Usage   : *INTERNAL Bio::DB::TFBS stuff*
        Function: Loads up (like use) a module at run time on demand