Unit

UNIT 2.6 Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence

  1. Jonathan Schug

Published Online: 1 FEB 2003

DOI: 10.1002/0471250953.bi0206s00

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Schug, J. 2003. Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence. Current Protocols in Bioinformatics. 2:2.6.

Author Information

  1. Center Of Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania

Publication History

  1. Published Online: 1 FEB 2003
  2. Published Print: JAN 2003

This is not the most recent version of the article. View current version (1 MAR 2008)

Abstract

This unit describes how to use the Transcription Element Search System (TESS). This Web site predicts transcription factor binding sites 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.