Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence

Jonathan Schug1

1 University of Pennsylvania, Philadelphia, Pennsylvania
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 2.6
DOI:  10.1002/0471250953.bi0206s21
Online Posting Date:  March, 2008
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Abstract

This unit describes how to use the Transcription Element Search System (TESS). This Web site predicts transcription factor binding sites (TFBS) in DNA sequence using two different kinds of models of sites, strings and positional weight matrices. The binding of transcription factors to DNA is a major part of the control of gene expression. Transcription factors exhibit sequence‐specific binding; they form stronger bonds to some DNA sequences than to others. Identification of a good binding site in the promoter for a gene suggests the possibility that the corresponding factor may play a role in the regulation of that gene. However, the sequences transcription factors recognize are typically short and allow for some amount of mismatch. Because of this, binding sites for a factor can typically be found at random every few hundred to a thousand base pairs. TESS has features to help sort through and evaluate the significance of predicted sites. Curr. Protoc. Bioinform. 21:2.6.1‐2.6.15. © 2008 by John Wiley & Sons, Inc.

Keywords: transcription factor; DNA sequence; genome; promoter; gene regulation

     
 
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Table of Contents

  • Basic Protocol 1: Predicting Transcription Factor Binding Sites
  • Guidelines for Understanding Results
  • Commentary
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
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Internet Resources
   http://www.pcbi.upenn.edu/tess
  The TESS Web site.
   http://www.biobase.de
  Web site for the company that now maintains TRANSFAC.
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