UNIT 2.1 An Introduction to Recognizing Functional Domains

  1. Gary D. Stormo

Published Online: 1 OCT 2006

DOI: 10.1002/0471250953.bi0201s15

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Stormo, G. D. 2006. An Introduction to Recognizing Functional Domains. Current Protocols in Bioinformatics. 15:2.1:2.1.1–2.1.5.

Author Information

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

Publication History

  1. Published Online: 1 OCT 2006
  2. Published Print: SEP 2006

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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., TRANSFAC). In addition, it reviews databases such as Pfam, InterPro and Blocks, which are available for protein analysis.


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