Comparative Genomics

Comparative Genomics, Volume 2, provides a collection of robust protocols for molecular biologists beginning to use comparative genomic analysis tools in a variety of areas. Volume 2 contains the last three of seven sections. In the second volume, the fifth section describes a number of tools for comparative analysis of domain and gene families. These tools are particularly useful for predicting protein function as well as potential protein-protein interactions. In the sixth section, methods for comparing groups of genes and gene order are discussed, as are several tools for analyzing genome evolution. Finally, the seventh section deals with experimental comparative genomics. This section includes methods for comparing gene copy number across an entire genome, comparative genomic hybridization, SNP analysis, as well as genome-wide mapping and typing systems for bacterial genomes. Given the tremendous increase in available biosequence data over the past ten years, Comparative Genomics, Volume 1, is timely, comprehensive, and novel. A companion Volume 1 is also available from Humana Press.

Provides a collection of robust protocols for molecular biologists studying comparative genomics Each chapter includes detailed instructions for using a particular tool or method and an introduction to the theory behind the technique A Notes section at the end of each chapter that guides the user through commonly encountered difficulties, providing key tips for using the method most efficiently

Inhalt
Preface v.- Contributors xi.- Table of ContentsVolume 1 xv.- I: Comparative Analysis of Domain and Protein Families.- 1 Computational Prediction of Domain Interactions 3Philipp Pagel, Normann Strack, Matthias Oesterheld, Volker Stümpflen, and Dmitrij Frishman 3.- 2 Domain Team: Synteny of Domains is a New Approach in Comparative Genomics 17Sophie Pasek 17.- 3 Inference of Gene Function Based on Gene Fusion Events: The Rosetta-Stone Method 31Karsten Suhre 31.- 4 Pfam: A Domain-Centric Method for Analyzing Proteins and Proteomes 43Jaina Mistry and Robert Finn 43.- 5 InterPro and InterProScan: Tools for Protein Sequence Classification and Comparison 59Nicola Mulder and Rolf Apweiler 59.- 6 Gene Annotation and Pathway Mapping in KEGG 71Kiyoko F. Aoki-Kinoshita and Minoru Kanehisa 71.- II:Orthologs, Synteny, and Genome Evolution.- 7 Ortholog Detection Using the Reciprocal Smallest Distance Algorithm 95Dennis P. Wall and Todd DeLuca 95.- 8 Finding Conserved Gene Order Across Multiple Genomes 111Giulio Pavesi and Graziano Pesole 111.- 9 Analysis of Genome Rearrangement by Block-Interchanges 121Chin Lung Lu, Ying Chih Lin, Yen Lin Huang, and Chuan Yi Tang 121.- 10 Analyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System 135Aaron E. Darling, Todd J. Treangen, Xavier Messeguer, and Nicole T. Perna 135.- 11 Visualization of Syntenic Relationships With SynBrowse 153Volker Brendel, Stefan Kurtz, and Xioakang Pan 153.- 12 Gecko and GhostFam: Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes 165Thomas Schmidt and Jens Stoye 165.- III:Experimental Analysis of Whole Genomes: A NALYSIS OF C OPY N UMBER AND S EQUENCE P OLYMORPHISMS.- 13 Genome-wide Copy Number Analysis on GeneChip® Platform Using Copy Number Analyzer for Affymetrix GeneChip2.0 Software 185Seishi Ogawa, Yasuhito Nanya, and Go Yamamoto 185.- 14 Oligonucleotide Array Comparative Genomic Hybridization 207Paul van den IJssel and Bauke Ylstra 207.- 15 Studying Bacterial Genome Dynamics Using Microarray-Based Comparative Genomic Hybridization 223Eduardo N. Taboada, Christian C. Luebbert, and John H. E. Nash 223.- 16 DNA Copy Number Data Analysis Using the CGHAnalyzer Software Suite 255Joel Greshock 255.- 17 Microarray-Based Approach for Genome-Wide Survey of Nucleotide Polymorphisms 267Brian W. Brunelle and Tracy L. Nicholson 267.- 18 High-Throughput Genotyping of Single Nucleotide Polymorphisms with High Sensitivity 281Honghua Li, Hui-Yun Wang, Xiangfeng Cui, Minjie Luo, Guohong Hu, Danielle M. Greenawalt, Irina V. Tereshchenko, James Y. Li, Yi Chu, and Richeng Gao 281.- 19 Single Nucleotide Polymorphism Mapping Array Assay 295Xiaofeng Zhou and David T. W. Wong 295.- 20 Molecular Inversion Probe Assay 315Farnaz Absalan and Mostafa Ronaghi 315.- 21 novoSNP3: Variant Detection and Sequence Annotation in Resequencing Projects 331Peter De Rijk and Jurgen Del-Favero 331.- 22 Rapid Identification of Single Nucleotide Substitutions Using SeqDoC 345Mark L. Crowe 345.- 23 SNPHunter: A Versatile Web-Based Tool for Acquiring and Managing Single Nucleotide Polymorphisms 359Tianhua Niu 359.- 24 Identification of Disease Genes: Example-Driven Web-Based Tutorial 371Medha Bhagwat 371.- 25 Variable Number Tandem Repeat Typing of Bacteria 395Siamak P. Yazdankhah and BjØrn-Arne Lindstedt 395.- 26 Fluorescent Amplified Fragment Length Polymorphism Genotyping of Bacterial Species 405Meeta Desai 407.- 27 FLP-Mapping: A Universal, Cost-Effective, and Automatable Method for Gene Mapping 419Knud Nairz, Peder Zipperlen, and Manuel Schneider 419.- Index 433.