TFBS::DB::TRANSFAC(3pm)
NAME
- TFBS::DB::TRANSFAC - interface to database of TRANSFAC public position
frequency matrices at TESS (http://www.cbil.upenn.edu/tess)
- -------------------------------- NOTICE ----------------------------------
The TRANSFAC database is free for non-commercial use. For commercial use
the TRANSFAC databases and programs have to be licensed. Please read
the DISCLAIMER at http://transfac.gbf.de/TRANSFAC/disclaimer.htm.
- -------------------------------------------------------------------------
SYNOPSIS
o creating a database object by connecting to TRANSFAC data
my $db = TFBS::DB::TRANSFAC->connect();
o retrieving a TFBS::Matrix::* object from the database
# retrieving a PFM by ID
my $pfm = $db->get_Matrix_by_ID('V$CEBPA_01','PFM');
#retrieving a PWM by TRANSFAC accession number
my $pwm = $db->get_Matrix_by_acc('M00116', 'PWM');
DESCRIPTION
- TFBS::DB::TRANSFAC is a read only database interface that fetches
TRANSFAC matrix data from TESS web interface
(http://www.cbil.upen.edu/TESS) and returns TFBS::Matrix::* objects.
- connect
- Title : connect
Usage : my $db = TFBS::DB::TRANSFAC->connect(%args);
Function: Creates a TRANSFAC database connection object, which can be used
to retrieve matrices from public TRANSFAC databases via the web
- Returns : a TFBS::DB::TRANSFAC object
Args : -proxy # OPTIONAL: a http proxy server name,
# usually required for accessing TRANSFAC from behind
# a firewall
- -accept_conditions # OPTIONAL: by setting this to a true
# value, you confirm that you
# have read and accepted the terms
# of use of TRANSFAC at
# http://transfac.gbf.de/TRANSFAC/disclaimer.htm;
# this also supresses the annoying
# message that is printed to STDERR
# upon invoking the method
- new
- Title : connect
Usage : my $db = TFBS::DB::TRANSFAC->connect(%args);
Function: Here, I<new> is just a synonim for I<connect>
(to make the interface consistent with other
bioperl read-obly Bio::DB::* objects)
Returns : a TFBS::DB::TRANSFAC object
Args : -accept_conditions # see explanation at I<new>
- get_Matrix_by_ID
- Title : get_Matrix_by_ID
Usage : my $pfm = $db->get_Matrix_by_ID('V$CREB_01', 'PFM');
Function: fetches matrix data under the given TRANSFAC ID from the
database and returns a TFBS::Matrix::* object
- Returns : a TFBS::Matrix::* object; the exact type of the
object depending on the second argument (allowed
values are 'PFM', 'ICM', and 'PWM'); returns undef if
matrix with the given ID is not found
- Args : (Matrix_ID, Matrix_type)
Matrix_ID is a string; Matrix_type is one of the
following: 'PFM' (raw position frequency matrix),
'ICM' (information content matrix) or 'PWM' (position
weight matrix)
If Matrix_type is omitted, a PFM is retrieved by default.
- get_Matrix_by_acc
- Title : get_Matrix_by_acc
Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM');
Function: fetches matrix data under the given TRANSFAC aaccession number
from database and returns a TFBS::Matrix::* object
- Returns : a TFBS::Matrix::* object; the exact type of the
object depending on the second argument (allowed
values are 'PFM', 'ICM', and 'PWM'); returns undef if
matrix with the given ID is not found
- Args : (Matrix_ID, Matrix_type)
Matrix_ID is a string; Matrix_type is one of the
following: 'PFM' (raw position frequency matrix),
'ICM' (information content matrix) or 'PWM' (position
weight matrix)
If Matrix_type is omitted, a PFM is retrieved by default.