UNIT 2.1 An Introduction to Recognizing Functional Domains

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.