Reference

TFBS::DB::TRANSFAC(3pm)

interface to database of TRANSFAC public position frequency matrices at TESS (http://www.cbil.upenn.edu/tess)

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

•

creating a database object by connecting to TRANSFAC data

    my $db = TFBS::DB::TRANSFAC->connect();
•

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 suppresses 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 accession 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.

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