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An Introduction to Recognizing Functional Domains

Gary D. Stormo¹

¹Washington 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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Introduction
Domain Representations
DNA Analyses
Protein Analyses
Literature Cited
Figures

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Figures

Figure 2.1.1

Binding site representation for CREB (M00178 from TRANSFAC using TESS, unit 2.6). (A) Alignment matrix that lists the number of times each base occurs at each position in a collection of 20 known binding sites. (B) Consensus sequence, showing the most common base at each position, or using ambiguous base representations when two bases are very common (see appendix 1A for IUPAC ambiguous base code). (C) Weight matrix for the set of sites, using the logarithms of the observed counts over those expected by chance. All numbers in the alignment matrix are increased by one as a small sample size correction. (D) The scores obtained with the matrix in C for two specific sequences. The scores are the sum of the bold numbers, corresponding to the base at each position in each sequence.

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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.