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
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library


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

PDF or HTML at Wiley Online Library

Table of Contents

  • Basic Protocol 1: Predicting Transcription Factor Binding Sites
  • Guidelines for Understanding Results
  • Commentary
  • Figures
  • Tables
PDF or HTML at Wiley Online Library


PDF or HTML at Wiley Online Library



Literature Cited

Literature Cited
   Berg, O.G. 1990. Base‐pair specificity of protein‐DNA recognition: A statistical‐mechanical model. Biomed. Biochim. Acta 49: 963‐975.
   Chen, Q.K., Hertz, G.Z., and Stormo, G.D. 1997. PromFD 1.0: A computer program that predicts eukaryotic pol II promoters using strings and IMD matrices. Comput. Appl. Biosci. 13: 29‐35.
   Day, W.H. and McMorris, F.R. 1992. Critical comparison of consensus methods for molecular sequences. Nucleic Acids Res. 20: 1093‐1099.
   Fitzwater, T. and Polisky, B. 1996. A SELEX primer. Methods Enzymol. 267: 275‐301.
   Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., and Haussler, A.D. 2002. The Human Genome Browser at UCSC. Genome Res. 12: 996‐1006.
   Loots, G.G., Ovcharenko, I., Pachter, L., Rubin, E., and Dubchak, I. 2002. rVISTA: A high throughput comparative approach to identifying eukaryotic transcriptional regulatory elements in noncoding genomic sequences. Genome Res. 12: 832‐839.
   Quandt, K., Frech, K., Karas, H., Wingender, E., and Werner, T. 1995. MatInd and MatInspector: New, fast, and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res. 23: 4878‐4884.
   Schug, J. and Overton, G.C. 1997. Modeling transcription factor binding sites with Gibbs sampling and the minimum description length encoding. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5: 268‐271.
   Schwartz, S., Zhang, Z., Frazer, K.A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R., and Miller, W. 2000. PipMaker: A Web server for aligning two genomic DNA sequences. Genome Res. 10: 577‐586.
   Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., and Lewis, S. 2002. The generic genome browser: A building block for a model organism system database. Genome Res. 12: 1599‐1610.
   Vlieghe, D., Sandelin, A., De Bleser, P.J., Vleminckx, K., Wasserman, W.W., van Roy, F., and Lenhard, B. 2006. A new generation of jaspar, the open‐access repository for transcription factor binding site profiles. Nucleic Acids Res. 34: D95‐D97.
   Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krull, M., Matys, V., Michael, H., Ohnhauser, R., Pruss, M., Schacherer, F., Thiele, S., and Urbach, S. 2001. The TRANSFAC system on gene expression regulation. Nucleic Acids Res. 29: 281‐283.
Internet Resources
  The TESS Web site.
  Web site for the company that now maintains TRANSFAC.
PDF or HTML at Wiley Online Library