Comparative Genomics

by Bergman, Nicholas H.

• ISBN13: 9781934115374
• ISBN10: 1934115371
• Format: Hardcover
• Copyright: 2007-12-20
• Publisher: Humana Pr Inc

Summary

This volume provides a collection of robust protocols for molecular biologists studying comparative genomics. Given the tremendous increase in available biosequence data over the past ten years, this volume is timely, comprehensive, and novel. The volume is intended for molecular biologists, biochemists and geneticists.

Table of Contents

Preface	p. v
Contributors	p. xi
Table of Contents-Volume 1	p. xv
Comparative Analysis of Domain and Protein Families
Computational Prediction of Domain Interactions	p. 3
Domain Team: Synteny of Domains is a New Approach in Comparative Genomics	p. 17
Inference of Gene Function Based on Gene Fusion Events: The Rosetta-Stone Method	p. 31
Pfam: A Domain-Centric Method for Analyzing Proteins and Proteomes	p. 43
InterPro and InterProScan: Tools for Protein Sequence Classification and Comparison	p. 59
Gene Annotation and Pathway Mapping in KEGG	p. 71
Orthologs, Synteny, and Genome Evolution
Ortholog Detection Using the Reciprocal Smallest Distance Algorithm	p. 95
Finding Conserved Gene Order Across Multiple Genomes	p. 111
Analysis of Genome Rearrangement by Block-Interchanges	p. 121
Analyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System	p. 135
Visualization of Syntenic Relationships With SynBrowse	p. 153
Gecko and GhostFam: Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes	p. 165
Experimental Analysis of Whole Genomes: Analysis of Copy Number and Sequence Polymorphisms
Genome-wide Copy Number Analysis on GeneChip Platform Using Copy Number Analyzer for Affymetrix GeneChip 2.0 Software	p. 185
Oligonucleotide Array Comparative Genomic Hybridization	p. 207
Studying Bacterial Genome Dynamics Using Microarray-Based Comparative Genomic Hybridization	p. 223
DNA Copy Number Data Analysis Using the CGHAnalyzer Software Suite	p. 255
Microarray-Based Approach for Genome-Wide Survey of Nucleotide Polymorphisms	p. 267
High-Throughput Genotyping of Single Nucleotide Polymorphisms with High Sensitivity	p. 281
Single Nucleotide Polymorphism Mapping Array Assay	p. 295
Molecular Inversion Probe Assay	p. 315
novoSNP3: Variant Detection and Sequence Annotation in Resequencing Projects	p. 331
Rapid Identification of Single Nucleotide Substitutions Using SeqDoC	p. 345
SNPHunter: A Versatile Web-Based Tool for Acquiring and Managing Single Nucleotide Polymorphisms	p. 359
Identification of Disease Genes: Example-Driven Web-Based Tutorial	p. 371
Variable Number Tandem Repeat Typing of Bacteria	p. 395
Fluorescent Amplified Fragment Length Polymorphism Genotyping of Bacterial Species	p. 407
FLP-Mapping: A Universal, Cost-Effective, and Automatable Method for Gene Mapping	p. 419
Index	p. 433
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