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Comparative Genomics

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. João C. Setubal

    1. Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil

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    You can also search for this editor in PubMed   Google Scholar

  2. Jens Stoye

    1. Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

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    You can also search for this editor in PubMed   Google Scholar

  3. Peter F. Stadler

    1. Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1704)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xii
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  2. Gene Phylogenies and Orthologous Groups

    • João C. Setubal, Peter F. Stadler
    Pages 1-28

  3. Pan-Genome Storage and Analysis Techniques

    • Tina Zekic, Guillaume Holley, Jens Stoye
    Pages 29-53

  4. Comparative Genomics for Prokaryotes

    • João C. Setubal, Nalvo F. Almeida, Alice R. Wattam
    Pages 55-78

  5. Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center

    • Alice R. Wattam, Thomas Brettin, James J. Davis, Svetlana Gerdes, Ronald Kenyon, Dustin Machi et al.
    Pages 79-101

  6. Phylogenomics

    • José S. L. Patané, Joaquim Martins Jr., João C. Setubal
    Pages 103-187

  7. Comparative Genome Annotation

    • Stefanie König, Lars Romoth, Mario Stanke
    Pages 189-212

  8. A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes

    • Danillo Oliveira Alvarenga, Leandro M. Moreira, Mick Chandler, Alessandro M. Varani
    Pages 213-242

  9. Comparative Metagenomics

    • Andrew Maltez Thomas, Felipe Prata Lima, Livia Maria Silva Moura, Aline Maria da Silva, Emmanuel Dias-Neto, João C. Setubal
    Pages 243-260

  10. Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches

    • Tom Hartmann, Martin Middendorf, Matthias Bernt
    Pages 261-289

  11. Whole Genome Duplication in Plants: Implications for Evolutionary Analysis

    • David Sankoff, Chunfang Zheng
    Pages 291-315

  12. Sequence-Based Synteny Analysis of Multiple Large Genomes

    • Daniel Doerr, Bernard M. E. Moret
    Pages 317-329

  13. Family-Free Genome Comparison

    • Daniel Doerr, Pedro Feijão, Jens Stoye
    Pages 331-342

  14. Comparative Methods for Reconstructing Ancient Genome Organization

    • Yoann Anselmetti, Nina Luhmann, Sèverine Bérard, Eric Tannier, Cedric Chauve
    Pages 343-362

  15. Comparative RNA Genomics

    • Rolf Backofen, Jan Gorodkin, Ivo L. Hofacker, Peter F. Stadler
    Pages 363-400

  16. Bioinformatic Approaches for Comparative Analysis of Viruses

    • Deyvid Amgarten, Chris Upton
    Pages 401-417

  17. Comparative Genomics of Gene Loss and Gain in Caenorhabditis and Other Nematodes

    • Christian Rödelsperger
    Pages 419-432

  18. Comparative Genomics in Drosophila

    • Martin Oti, Attilio Pane, Michael Sammeth
    Pages 433-450

  19. Comparative Genomics in Homo sapiens

    • Martin Oti, Michael Sammeth
    Pages 451-472

  20. Back Matter

    Pages 473-481
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Keywords

About this book

This volume provides broad coverage of computational and mathematical techniques and concepts related to the field of comparative genomics. The topics covered in the chapters range from those concerned with general techniques and concepts that apply to all organisms to others that are more specialized, covering specific biological systems such as viruses, Drosophila, and Homo sapiens. Written in the highly successful Methods in Molecular Biology series format, by authors who are active researchers in the field, many chapters include step-by-step procedures, which illustrate practical applications of the techniques described.

Cutting-edge and thorough, Comparative Genomics: Methods and Protocols should be useful to students and researchers in the continually growing and exciting field of comparative genomics.



Editors and Affiliations

  • Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil

    João C. Setubal

  • Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

    Jens Stoye

  • Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

    Peter F. Stadler

Bibliographic Information

  • Book Title: Comparative Genomics

  • Book Subtitle: Methods and Protocols

  • Editors: João C. Setubal, Jens Stoye, Peter F. Stadler

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7463-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2018

  • Hardcover ISBN: 978-1-4939-7461-0Published: 26 December 2017

  • Softcover ISBN: 978-1-4939-8493-0Published: 30 August 2018

  • eBook ISBN: 978-1-4939-7463-4Published: 23 December 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 481

  • Number of Illustrations: 27 b/w illustrations, 68 illustrations in colour

  • Topics: Human Genetics

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