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• Introduction
• Installing the TRANSFAC plugin and files
• Annotate with TRANSFAC Information
  • Output
• Install and uninstall plugins
  • Install
  • Uninstall
• Bibliography

Introduction

The TRANSFAC plugin can be used to search for putative transcription factor binding sites in DNA sequences.

The binding site predictions are done by the Match^TM tool, which uses the positional weight matrix library from TRANSFAC^® to analyze your sequences.^1.1 For each of these matrices, Match contains optimized parameters, for minimization of error rates (false negative rate and false positive rate).

As a special feature, Match provides the option to use profiles that are specific subsets of matrices with optimized cut-offs. These profiles allow users to adapt Match to their specific interests. For example, promoters of a certain tissue can be searched with tissue-specific profiles. In addition to several pre-defined profiles provided in the TRANSFAC plugin, you can create your own profiles in the online version of TRANSFAC. The matrices in the result list of the TRANSFAC plugin are hyperlinked to the respective Matrix Reports in the TRANSFAC online version.

In order to be able to use the TRANSFAC plugin you need to:

• Download and install the files relevant for TRANSFAC from geneXplain on your computer. You will need a download subscription of TRANSFAC from geneXplain to do this (see http://genexplain.com/transfac/).
• Install the TRANSFAC plugin into your workbench.
• Configure the Preferences in your workbench so that the TRANSFAC plugin knows where to find the TRANSFAC data and binaries.

We cover the above topics first in this manual, and following that, provide information on carrying out searches of TRANSFAC via the CLC Workbench.

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Footnotes

... sequences.^1.1

TRANSFAC is a registered trademark of QIAGEN

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