Plant Bioinformatics

Methods and Protocols

  • David Edwards

Part of the Methods in Molecular Biology™ book series (MIMB, volume 406)

Table of contents

  1. Front Matter
    Pages i-xv
  2. Peter Sterk, Tamara Kulikova, Paul Kersey, Rolf Apweiler
    Pages 1-21
  3. David Wheeler
    Pages 23-59
  4. Tatiana Tatusova, Brian Smith-White, James Ostell
    Pages 61-87
  5. Emmanuel Boutet, Damien Lieberherr, Michael Tognolli, Michel Schneider, Amos Bairoch
    Pages 89-112
  6. Agnes P. Chan, Pablo D. Rabinowicz, John Quackenbush, C. Robin Buell, Chris D. Town
    Pages 113-136
  7. Manuel Spannagl, Georg Haberer, Rebecca Ernst, Heiko Schoof, Klaus F. X. Mayer
    Pages 137-159
  8. Timothy J. Close, Steve Wanamaker, Mikeal L. Roose, Matthew Lyon
    Pages 161-177
  9. Rebecca L. Poole
    Pages 179-212
  10. Nick James, Neil Graham, Debbie Clements, Beatrice Schildknecht, Sean May
    Pages 213-227
  11. Christopher G. Love, David Edwards
    Pages 229-243
  12. Michael D. Gonzales, Kamal Gajendran, Andrew D. Farmer, Eric Archuleta, William D. Beavis
    Pages 245-259
  13. Ernest F. Retzel, James E. Johnson, John A. Crow, Anne F. Lamblin, Charles E. Paule
    Pages 261-274
  14. Ximiao He, Jun Wang
    Pages 275-299
  15. Helen O’Sullivan
    Pages 301-314
  16. Doreen Ware
    Pages 315-329
  17. Carolyn J. Lawrence
    Pages 331-345
  18. Roger P. Wise, Rico A. Caldo, Lu Hong, Lishuang Shen, Ethalinda Cannon, Julie A. Dickerson
    Pages 347-363
  19. Stephen J. Robinson, Justin D. Guenther, Christopher T. Lewis, Matthew G. Links, Isobel A.P. Parkin
    Pages 365-386
  20. Kan Nobuta, Kalyan Vemaraju, Blake C. Meyers
    Pages 387-407
  21. Lloyd W Sumner, Ewa Urbanczyk-Wochniak, Corey D Broeckling
    Pages 409-436
  22. Ali Masoudi-Nejad, Susumu Goto, Takashi R. Endo, Minoru Kanehisa
    Pages 437-458
  23. Arllet Portugal, Ranjan Balachandra, Thomas Metz, Richard Bruskiewich, Graham McLaren
    Pages 459-471
  24. Emily Dimmer, Tanya Z. Berardini, Daniel Barrell, Evelyn Camon
    Pages 495-520
  25. Volker Brendel
    Pages 521-533
  26. Jason E. Stajich
    Pages 535-548
  27. Back Matter
    Pages 549-552

About this book


Bioinformatics is a new and rapidly evolving field of research that is being driven by the development and application of various ‘omics technologies. Plant Bioinformatics focuses on applied bioinformatics with specific applications to crops and model plants. Chapters in this new volume are aimed at researchers developing bioinformatics databases and tools, detailing commonly applied database formats and biology-focused scripting languages. These will provide both beginners and experienced bioinformatics researchers with the necessary skills to develop and apply bioinformatics tools for their specialist area of plant research. Each chapter includes practical examples and highlight common problems encountered in bioinformatics analysis. Protocols in this volume detail EMBL Nucleotide Sequence, TAIR database, VarvEST, MIPS, BGI-RIS V2, BarleyBase/PLEXdb, SAGE, KEGG, and more. Plant biologists who have an interest in or requirement for the accessing and manipulation of the huge amount of data being generated by high throughput technologies will find this new volume to be an immeasurable aid in their research.


Annotation Ensembl Gene Ontology National Center for Biotechnology Information bioinformatics biotechnology databases genetics genome plant pathogens

Editors and affiliations

  • David Edwards
    • 1
  1. 1.Primary Industries Research Victoria, Plant Genetics and Genomics,Victorian AgriBiosciences Centre, La Trobe UniversityBundooraAustralia

Bibliographic information

  • DOI
  • Copyright Information Humana Press 2007
  • Publisher Name Humana Press
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-58829-653-5
  • Online ISBN 978-1-59745-535-0
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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