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Bio::DB::TFBS(3) User Contributed Perl Documentation Bio::DB::TFBS(3)
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:
http://bugzilla.open-bio.org/
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
perl v5.14.1 2011-07-22 Bio::DB::TFBS(3)
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