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 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.