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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

•

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.