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Comparative Genomics

Volume 2

  • Book
  • © 2007

Overview

Editors:
  1. Nicholas H. Bergman

    1. Bioinformatics Program and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor

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  • 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

Part of the book series: Methods in Molecular Biology (MIMB, volume 396)

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Table of contents (27 protocols)

  1. Front Matter

    Pages i-xviii
    Download chapter PDF

  2. Comparative Analysis of Domain and Protein Families

    1. Front Matter

      Pages 1-1
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    2. Computational Prediction of Domain Interactions

      • Philipp Pagel, Normann Strack, Matthias Oesterheld, Volker Stümpflen, Dmitrij Frishman
      Pages 3-15

    3. Domain Team

      • Sophie Pasek
      Pages 17-29

    4. Inference of Gene Function Based on Gene Fusion Events

      • Karsten Suhre
      Pages 31-41

    5. Pfam

      • Jaina Mistry, Robert Finn
      Pages 43-58

    6. InterPro and InterProScan

      • Nicola Mulder, Rolf Apweiler
      Pages 59-70

    7. Gene Annotation and Pathway Mapping in KEGG

      • Kiyoko F Aoki-Kinoshita, Minoru Kanehisa
      Pages 71-91

  3. Orthologs, Synteny, and Genome Evolution

    1. Front Matter

      Pages 93-93
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    2. Ortholog Detection Using the Reciprocal Smallest Distance Algorithm

      • Dennis P. Wall, Todd DeLuca
      Pages 95-110

    3. Finding Conserved Gene Order Across Multiple Genomes

      • Giulio Pavesi, Graziano Pesole
      Pages 111-119

    4. Analysis of Genome Rearrangement by Block-Interchanges

      • Lung Lu Chin, Chih Lin Ying, Lin Huang Yen, Yi Tang Chuan
      Pages 121-134

    5. Analyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System

      • Aaron E Darling, Todd J Treangen, Xavier Messeguer, Nicole T Perna
      Pages 135-152

    6. Visualization of Syntenic Relationships With SynBrowse

      • Volker Brendel, Stefan Kurtz, Xioakang Pan
      Pages 153-163

    7. Gecko and GhostFam

      • Thomas Schmidt, Jens Stoye
      Pages 165-182

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

    1. Front Matter

      Pages 183-183
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    2. Genome-wide Copy Number Analysis on GeneChip® Platform Using Copy Number Analyzer for Affymetrix GeneChip 2.0 Software

      • Seishi Ogawa, Yasuhito Nanya, Go Yamamoto
      Pages 185-206

    3. Oligonucleotide Array Comparative Genomic Hybridization

      • Paul van den IJssel, Bauke Ylstra
      Pages 207-221

    4. Studying Bacterial Genome Dynamics Using Microarray-Based Comparative Genomic Hybridization

      • Eduardo N. Taboada, Christian C. Luebbert, John H.E. Nash
      Pages 223-253

    5. DNA Copy Number Data Analysis Using the CGHAnalyzer Software Suite

      • Joel Greshock
      Pages 255-266
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Keywords

About this book

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.

Editors and Affiliations

  • Bioinformatics Program and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor

    Nicholas H. Bergman

Bibliographic Information

  • Book Title: Comparative Genomics

  • Book Subtitle: Volume 2

  • Editors: Nicholas H. Bergman

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-59745-515-2

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2007

  • Hardcover ISBN: 978-1-934115-37-4Published: 29 November 2007

  • Softcover ISBN: 978-1-61737-933-8Published: 25 December 2011

  • eBook ISBN: 978-1-59745-515-2Published: 07 February 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVIII, 434

  • Number of Illustrations: 150 b/w illustrations, 1 illustrations in colour

  • Topics: Biochemistry, general, Human Genetics, Cell Biology

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