Prediction of the binding specificity of transcription factors using support vector regression.

Johannes Eichner1, Adrian Schröder1, Andreas Dräger1, Jonas Eichner1, Jochen Supper1, Dierk Wanke2, Klaus Harter2 Andreas Zell1

1Center for Bioinformatics Tübingen (ZBIT), Germany, 2Center for Plant Physiology Tübingen (ZMBP), Germany


Short description:
SABINE is a tool to predict the binding specificity of a transcription factor (TF), given its amino acid sequence, species, structural superclass and DNA-binding domains. For convenience, the superclass and DNA-binding domains of a given TF can be predicted based on sequence homology with TFs in the training set of SABINE. Alternatively, the tool TFpredict, which predicts all structural characteristics of TFs required by SABINE, can be employed in an additional preprocessing step. SABINE compares a given factor to a predefined set of TFs of the same superclass for which experimentally confirmed position frequency matrices (PFM) are available. Based on various features capturing evolutionary, structural and physicochemical similarity of the DNA-binding domains, the PFM similarity is predicted by means of support vector regression. The TFs with highest PFM similarity to the factor of interest are reported and their PFMs are merged using STAMP to generate the predicted consensus PFM.


Availability:
SABINE is available in two different versions:

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

SABINE webservice SABINE stand-alone

License:

GPL version 3 SABINE 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

   
SABINE 1.2 released: A new version of SABINE with updated training data is now available.   -   (eichner - 2013-22-05 17:13)
   
SABINE 1.1 released: A new version of SABINE providing various features, which simplify the installation and use of the tool, is now available. See the Release Notes on our download page for an overview of the new features of SABINE.   -   (eichner - 2012-05-04 14:15)
   
Documentation: A complete documentation is now available.   -   (eichner - 2009-09-05 11:03)
   
Download: The stand-alone version of SABINE is available for download.   -   (eichner - 2009-09-20 15:32)
   
Webservice: The webservice version of SABINE is now available.   -   (eichner - 2009-10-01 13:19)

 

This project is promoted by:

BMBF Spher4Sys Virtual Liver ZBIT