An Introduction to Recognizing Functional Domains

Gary D. Stormo1

1 Washington University School of Medicine, St. Louis, Missouri
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 2.1
DOI:  10.1002/0471250953.bi0201s34
Online Posting Date:  June, 2011
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Abstract

This unit provides an overview of issues involved in domain recognition in protein and DNA sequences. It opens with a discussion of the two primary methods of domain representation, namely consensus sequences and alignment matrices (e.g., the log‐odds matrix). The unit continues with a brief overview of some of the resources available for identifying functional domains in nucleotide sequences (e.g., transcription factor binding sites). In addition, it reviews databases such as Pfam and InterPro, which are available for protein analysis. Curr. Protoc. Bioinform. 34:2.1.1‐2.1.6. © 2011 by John Wiley & Sons, Inc.

Keywords: functional domains; protein domains; transcription factor binding sites; regulatory sites; promoters

     
 
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Table of Contents

  • Introduction
  • Domain Representations
  • DNA Analyses
  • Protein Analyses
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

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Literature Cited

Literature Cited
   Eddy, S.R. 1998. Profile hidden Markov models. Bioinformatics 14:755‐763.
   Portales‐Casamar, E., Thongjuea, S., Kwon, A.T., Arenillas, D., Zhao, X., Valen, E., Yusuf, D., Lenhard, B., Wasserman, W.W., and Sandelin, A. 2010. JASPAR 2010: The greatly expanded open‐access database of transcription factor binding profiles. Nucleic Acids Res. 38:D105‐D110.
   Stormo, G.D. 2000. DNA binding sites: Representation and discovery. Bioinformatics 16:16‐23.
   Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krull, M., Matys, V., Michael, H., Ohnhäuser, R., Prüss, M., Schacherer, F., Thiele, S., and Urbach, S. 2001. The TRANSFAC system on gene expression regulation. Nucl. Acids Res. 29:281‐283.
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