---
name: "TFBS::DB::TRANSFAC"
section: "3pm"
platform: "linux"
package: "libtfbs-perl"
version: "0.7.1+ds-4+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/TFBS::DB::TRANSFAC"
---

# 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.
```