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Eukaryotic Genomic Databases

Methods and Protocols

Editors:

  • 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 1757)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xvi
  2. An Introduction to the Saccharomyces Genome Database (SGD)

    • Olivia W. Lang, Robert S. Nash, Sage T. Hellerstedt, Stacia R. Engel, The SGD Project
    Pages 21-30
  3. Using the Candida Genome Database

    • Marek S. Skrzypek, Jonathan Binkley, Gavin Sherlock
    Pages 31-47
  4. PomBase: The Scientific Resource for Fission Yeast

    • Antonia Lock, Kim Rutherford, Midori A. Harris, Valerie Wood
    Pages 49-68Open Access
  5. EuPathDB: The Eukaryotic Pathogen Genomics Database Resource

    • Susanne Warrenfeltz, Evelina Y. Basenko, Kathryn Crouch, Omar S. Harb, Jessica C. Kissinger, David S. Roos et al.
    Pages 69-113
  6. The Ensembl Genome Browser: Strategies for Accessing Eukaryotic Genome Data

    • Victoria Newman, Benjamin Moore, Helen Sparrow, Emily Perry
    Pages 115-139Open Access
  7. A Primer for the Rat Genome Database (RGD)

    • Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Jennifer R. Smith, Victoria Petri, Matthew J. Hoffman et al.
    Pages 163-209
  8. Bovine Genome Database: Tools for Mining the Bos taurus Genome

    • Darren E. Hagen, Deepak R. Unni, Aditi Tayal, Gregory W. Burns, Christine G. Elsik
    Pages 211-249
  9. Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database

    • Christina James-Zorn, Virgilio Ponferrada, Malcolm E. Fisher, Kevin Burns, Joshua Fortriede, Erik Segerdell et al.
    Pages 251-305
  10. Using ZFIN: Data Types, Organization, and Retrieval

    • Ceri E. Van Slyke, Yvonne M. Bradford, Douglas G. Howe, David S. Fashena, Sridhar Ramachandran, Leyla Ruzicka et al.
    Pages 307-347
  11. EchinoBase: Tools for Echinoderm Genome Analyses

    • Gregory A. Cary, R. Andrew Cameron, Veronica F. Hinman
    Pages 349-369
  12. A Multi-Omics Database for Parasitic Nematodes and Trematodes

    • John Martin, Rahul Tyagi, Bruce A. Rosa, Makedonka Mitreva
    Pages 371-397
  13. Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes

    • Christian Grove, Scott Cain, Wen J. Chen, Paul Davis, Todd Harris, Kevin L. Howe et al.
    Pages 399-470
  14. Using WormBase ParaSite: An Integrated Platform for Exploring Helminth Genomic Data

    • Bruce J. Bolt, Faye H. Rodgers, Myriam Shafie, Paul J. Kersey, Matthew Berriman, Kevin L. Howe
    Pages 471-491
  15. Using FlyBase to Find Functionally Related Drosophila Genes

    • Alix J. Rey, Helen Attrill, Steven J. Marygold, The FlyBase Consortium
    Pages 493-512
  16. Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects

    • Christine G. Elsik, Aditi Tayal, Deepak R. Unni, Gregory W. Burns, Darren E. Hagen
    Pages 513-556
  17. Navigating the i5k Workspace@NAL: A Resource for Arthropod Genomes

    • Monica F. Poelchau, Mei-Ju May Chen, Yu-Yu Lin, Christopher P. Childers
    Pages 557-577
  18. Back Matter

    Pages 579-581

About this book

This volume explores databases containing genome-based data and genome-wide analyses. This book covers databases from all eukaryotic taxa, except plants. The chapters describe database contents and classic use-cases, which assist in accessing eukaryotic genomic data and encouraging comparative genomic research. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and authoritative, Eukaryotic Genomic Databases: Methods and Protocols is a valuable resource for geneticists and molecular biologists who are interested in the latest eukaryotic genomics data.

The chapters 'PomBase: The Scientific Resource for Fission Yeast' and 'The Ensembl Genome Browser: Strategies for Accessing Eukaryotic Genome Data' are available open access under a CC BY 4.0 license via link.springer.com.

Editors and Affiliations

  • Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany

    Martin Kollmar

Bibliographic Information

  • Book Title: Eukaryotic Genomic Databases

  • Book Subtitle: Methods and Protocols

  • Editors: Martin Kollmar

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7737-6

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2018

  • Hardcover ISBN: 978-1-4939-7736-9Published: 15 May 2018

  • Softcover ISBN: 978-1-4939-9270-6Published: 10 December 2019

  • eBook ISBN: 978-1-4939-7737-6Published: 14 May 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVI, 581

  • Number of Illustrations: 2 b/w illustrations, 257 illustrations in colour

  • Topics: Human Genetics

Buy it now

Buying options

eBook USD 119.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 159.00
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access