Identification and structural characterization of transcription factors based on supervised machine learning.

Johannes Eichner*1, Florian Topf*1, Adrian Schröder1, Dierk Wanke2, Klaus Harter2, Andreas Zell1

1Center for Bioinformatics Tübingen (ZBIT), Germany, 2Center for Plant Physiology Tübingen (ZMBP), Germany
* These two authors contributed equally to this work.


Short description:
TFpredict is a tool which implements a novel three-step classification method which expects a protein sequence as input and (1) distinguishes transcription factors (TF) from other proteins (Non-TF), (2) predicts the structural superclass of TFs (see TransFac classification), and (3) identifies the DNA-binding domains of TFs. The latter two classification steps are only be performed if the given protein sequence was identified as a TF. The tool incorporates the results from a BLAST+ search into a novel feature representation which allows TF/non-TF classification by state-of-the-art machine learning methods. Specific supervised classifiers were contructed for the task of identifying TFs and their structural superclasses, respectively. Next, known protein domains are detected by the tool InterProScan and then the DNA-binding domains among these are filtered by means of GO-terms. TFpredict was implemented as a supplementary preprocessing tool for SABINE, which predicts the DNA-motif bound by a transcription factor, given its amino acid sequence, superclass, DNA-binding domains and organism.


Availability:
TFpredict is available in two different versions:

TFpredict webservice: In order to provide a convenient way of using TFpredict without local installation, we integrated the tool into our webservice framework.
TFpredict stand-alone: If you prefer to install the tool locally, you can download the latest stand-alone version of TFpredict at our download section.

TFpredict webservice TFpredict stand-alone

License:

GPL version 3 TFpredict is subject to the GNU General Public License 3.0. Visit our download section for a more detailed description of the license and the terms of use of this software.



info

New version: Version 1.3 is now available. The new version now uses the new InterproScan 5 web interface.   -   (roemer - 2015-04-27 12:00)
Documentation: A complete documentation is now available.   -   (eichner - 2013-04-08 17:36)
   
Download: The stand-alone version of TFpredict is available for download.   -   (eichner - 2013-04-06 13:59)
   
Webservice: The webservice version of TFpredict is now available.   -   (eichner - 2013-04-02 18:53)

 

This project is promoted by:

BMBF Spher4Sys Virtual Liver ZBIT