Preface v

Contributors xiii

1 Use of Genome Browsers to Locate Your Favorite Genes

Minou Bina 1

2 Methods for Identifying and Mapping Recent Segmental and Gene Duplications in Eukaryotic Genomes Razi Khaja, Jeffrey R. MacDonald, Junjun Zhang, and Stephen W. Scherer 9

3 Identification and Mapping of Paralogous Genes on a Known Genomic DNA Sequence Minou Bina 21

4 Quantitative DNA Fiber Mapping in Genome Research and Construction of Physical Maps Heinz-Ulrich G . Weier and Lisa W. Chu 31

5 PRINS for Mapping Single-Copy Genes

Avirachan T. Tharapel and Stephen S. Wachtel 59

6 VISTA Family of Computational Tools for Comparative Analysis of DNA Sequences and Whole Genomes Inna Dubchak and Dmitriy V. Ryaboy 69

7 Computational Prediction of cis-Regulatory Modules from Multispecies Alignments Using Galaxy, Table Browser, and GALA Laura Elnitski, David King, and Ross C. Hardison 91

8 Comparative Promoter Analysis in Vertebrate Genomes with the CORG Workbench Christoph Dieterich and Martin Vingron 105

9 cis-Regulatory Region Analysis Using BEARR VinsensiusBerlian Vega 119

10 A Database of 9-Mers from Promoter Regions of Human Protein-Coding Genes Minou Bina, Phillip Wyss,and Syed Rehan Shah 129

11 A Program Toolkit for the Analysis of Regulatory

Regions of Genes

Phillip Wyss, Sheryl A. Lazarus, and Minou Bina 135

12 Analysis of Allele-Specific Gene Expression

Julian C. Knight 153

13 Construction of microRNA-Containing Vectors for Expression in Mammalian Cells Yoko Fukuda, Hiroaki Kawasaki, and Kazunari Taira 167

14 Mining Microarray Data at NCBI's Gene

Expression Omnibus (GEO) Tanya Barrett and Ron Edgar 175

15 The Stanford Microarray Database: A User's Guide

Jeremy Gollub, Catherine A. Ball, and Gavin Sherlock 191

16 Detecting Nucleosome Ladders on Unique DNA Sequences in Mouse Liver Nuclei Tomara J. Fleury, Alfred Cioffi, and Arnold Stein 209

17 DNA Methyltransferase Probing of DNA-Protein Interactions

Scott A. Hoose and Michael P. Kladde 225

18 Protein Binding Microarrays (PBMs) for Rapid,

High-Throughput Characterization of the Sequence Specificities of DNA Binding Proteins Michael F. Berger and Martha L. Bulyk 245

19 Quantitative Profiling of Protein-DNA Binding on Microarrays Jiannis Ragoussis, Simon Field, and Irina A. Udalova 261

20 Analysis of Protein-DNA Binding by Streptavidin-Agarose Pulldown Kenneth K.Wu 281

21 Isolation and Mass Spectrometry of Specific

DNA Binding Proteins Mariana Yaneva and Paul Tempst 291

22 Isolation of Transcription Factor Complexes by In Vivo Biotinylation Tagging and Direct Binding to Streptavidin Beads Patrick Rodriguez, Harald Braun, Katarzyna E. Kolodziej, Ernie de Boer, Jennifer Campbell, Edgar Bonte,

Frank Grosveld, Sjaak Philipsen, and John Strouboulis 305

Index 325

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