Main description:

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.

Contents:

Preface...

Table of Contents...

Contributing Authors...

1. Identifying Sequenced Eukaryotic Genomes and Transcriptomes with diArk

Martin Kollmar and Dominic Simm

2. An Introduction to the Saccharomyces Genome Database (SGD)

Olivia W. Lang, Robert S. Nash, Sage T. Hellerstedt, Stacia R. Engel, and the SGD Project

3. Using the Candida Genome Database

Marek S. Skrzypek, Jonathan Binkley, and Gavin Sherlock

4. PomBase: The Scientific Resource for Fission Yeast

Antonia Lock, Kim Rutherford, Midori A. Harris, and Valerie Wood

5. EuPathDB: The Eukaryotic Pathogen Genomics Database Resource

Susanne Warrenfeltz, Evelina Y. Basenko, Kathryn Crouch, Omar S. Harb, Jessica C. Kissinger, David S. Roos, Achchuthan Shanmugasundram, and Fatima Silva-Franco

6. The Ensembl Genome Browser: Strategies for Accessing Eukaryotic Genome Data

Victoria Newman, Benjamin Moore, Helen Sparrow, and Emily Perry

7. Mouse Genome Informatics (MGI) is the International Resource for Information on the Laboratory Mouse

MeiYee Law and David R. Shaw

8. 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, Jeff De Pons, Marek A. Tutaj, Omid Ghiasvand, Monika Tutaj, Jyothi Thota, Melinda R. Dwinell, and Mary Shimoyama

9. Bovine Genome Database: Tools for Mining the Bos taurus Genome

Darren E. Hagen, Deepak R. Unni, Aditi Tayal, Gregory W. Burns, and Christine G. Elsik

10. Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database

Christina James-Zorn, Virgilio Ponferrada, Malcolm E. Fisher, Kevin Burns, Joshua Fortriede, Eri Segerdell, Kamran Karimi, Vaneet Lotay, Dong Zhou Wang, Stanley Chu, Troy Pells, Ying Wang, Peter D. Vize, and Aaron Zorn

11. Using ZFIN: Data Types, Organization and Retrieval

Ceri E. Van Slyke, Yvonne M. Bradford, Douglas G. Howe, David S. Fashena, Sridhar Ramachandran, Leyla Ruzicka, and ZFIN Staff

12. EchinoBase: Tools for Echinoderm Genome Analyses

Gregory A. Cary, Andy Cameron, and Veronia F. Hinman

13. A Multi-Omics Database for Parasitic Nematodes and Trematodes

John Martin, Rahul Tyagi, Bruce A. Rosa, and Makedonka Mitreva

14. Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes

Christian Grove, Scott Cain, Wen J. Chen, Paul Davis, Todd Harris, Kevin Howe, Ranjana Kishore, Raymond Lee, Michael Paulini, Daniela Raciti, Mary Ann Tuli, Kimberly Van Auken, Gary Williams, and the The WormBase Consortium

15. Using WormBase ParaSite: An Integrated Platform for Exploring Helminth Genomic Data

Bruce J. Bolt, Faye H. Rodgers, Myriam Shafie, Paul J. Kersey, Matthew Berriman, and Kevin L. Howe

16. Using FlyBase to Find Functionally Related Drosophila Genes

Alix J. Rey, Helen Attrill, Steven J. Marygold, and the FlyBase Consortium

17. Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects

Christine G. Elsik, Aditi Tayal, Deepak R. Unni, Gregory W. Burns, and Darren E. Hagen

18. Navigating the i5k Workspace@NAL: A Resource for Arthropod Genomes

Monica F. Poelchau, Mei-Ju May Chen, Yu-Yu Lin, and Christopher P. Childers