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