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

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