UNIT 2.1 An Introduction to Recognizing Functional Domains

  1. Gary D. Stormo

Published Online: 1 JUN 2011

DOI: 10.1002/0471250953.bi0201s34

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Stormo, G. D. 2011. An Introduction to Recognizing Functional Domains. Current Protocols in Bioinformatics. 34:2.1:2.1.1–2.1.6.

Author Information

  1. Washington University School of Medicine, St. Louis, Missouri

Publication History

  1. Published Online: 1 JUN 2011
  2. Published Print: JUN 2011


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.


  • functional domains;
  • protein domains;
  • transcription factor binding sites;
  • regulatory sites;
  • promoters