Comparative Genomics

Editors:

ISBN: 978-1-934115-37-4 (Print) 978-1-59745-515-2 (Online)

Table of contents (27 protocols)

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  1. Front Matter

    Pages i-xviii

  2. Comparative Analysis of Domain and Protein Families

    1. Front Matter

      Pages 1-1

    2. No Access

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      Pages 3-15

      Computational Prediction of Domain Interactions

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      Pages 17-29

      Domain Team

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      Pages 31-41

      Inference of Gene Function Based on Gene Fusion Events

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      Pages 43-58

      Pfam

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      Pages 59-70

      InterPro and InterProScan

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      Pages 71-91

      Gene Annotation and Pathway Mapping in KEGG

  3. Orthologs, Synteny, and Genome Evolution

    1. Front Matter

      Pages 93-93

    2. No Access

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      Pages 95-110

      Ortholog Detection Using the Reciprocal Smallest Distance Algorithm

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      Pages 111-119

      Finding Conserved Gene Order Across Multiple Genomes

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      Pages 121-134

      Analysis of Genome Rearrangement by Block-Interchanges

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      Pages 135-152

      Analyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System

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      Pages 153-163

      Visualization of Syntenic Relationships With SynBrowse

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      Pages 165-182

      Gecko and GhostFam

  4. Experimental Analysis of Whole Genomes: Analysis of Copy Number and Sequence Polymorphisms

    1. Front Matter

      Pages 183-183

    2. No Access

      Book Protocol

      Pages 185-206

      Genome-wide Copy Number Analysis on GeneChip® Platform Using Copy Number Analyzer for Affymetrix GeneChip 2.0 Software

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      Pages 207-221

      Oligonucleotide Array Comparative Genomic Hybridization

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      Pages 223-253

      Studying Bacterial Genome Dynamics Using Microarray-Based Comparative Genomic Hybridization

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      Pages 255-266

      DNA Copy Number Data Analysis Using the CGHAnalyzer Software Suite

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      Pages 267-279

      Microarray-Based Approach for Genome-Wide Survey of Nucleotide Polymorphisms

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      Pages 281-294

      High-Throughput Genotyping of Single Nucleotide Polymorphisms with High Sensitivity

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      Pages 295-314

      Single Nucleotide Polymorphism Mapping Array Assay

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      Pages 315-330

      Molecular Inversion Probe Assay

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