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Plant Bioinformatics

Methods and Protocols

  • Book
  • © 2007

Overview

Editors:
  1. David Edwards

    1. Primary Industries Research Victoria, Plant Genetics and Genomics,Victorian AgriBiosciences Centre, La Trobe University, Bundoora, Australia

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  • Aims to assist research scientists in choosing the most applicable database or bioinformatics tools to aid and promote their research in plant biotechnology
  • Chapters include practical examples and highlight common problems encountered in bioinformatics analysis

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

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Table of contents (26 protocols)

  1. Front Matter

    Pages i-xv
    Download chapter PDF

  2. The EMBL Nucleotide Sequence and Genome Reviews Databases

    • Peter Sterk, Tamara Kulikova, Paul Kersey, Rolf Apweiler
    Pages 1-21

  3. Using GenBank

    • David Wheeler
    Pages 23-59

  4. A Collection of Plant-Specific Genomic Data and Resources at NCBI

    • Tatiana Tatusova, Brian Smith-White, James Ostell
    Pages 61-87

  5. UniProtKB/Swiss-Prot

    • Emmanuel Boutet, Damien Lieberherr, Michael Tognolli, Michel Schneider, Amos Bairoch
    Pages 89-112

  6. Plant Database Resources at The Institute for Genomic Research

    • Agnes P. Chan, Pablo D. Rabinowicz, John Quackenbush, C. Robin Buell, Chris D. Town
    Pages 113-136

  7. MIPS Plant Genome Information Resources

    • Manuel Spannagl, Georg Haberer, Rebecca Ernst, Heiko Schoof, Klaus F. X. Mayer
    Pages 137-159

  8. HarvEST

    • Timothy J. Close, Steve Wanamaker, Mikeal L. Roose, Matthew Lyon
    Pages 161-177

  9. The TAIR Database

    • Rebecca L. Poole
    Pages 179-212

  10. AtEnsEMBL

    • Nick James, Neil Graham, Debbie Clements, Beatrice Schildknecht, Sean May
    Pages 213-227

  11. Accessing Integrated Brassica

    • Christopher G. Love, David Edwards
    Pages 229-243

  12. Leveraging Model Legume Information to Find Candidate Genes for Soybean Sudden Death Syndrome Using the Legume Information System

    • Michael D. Gonzales, Kamal Gajendran, Andrew D. Farmer, Eric Archuleta, William D. Beavis
    Pages 245-259

  13. Legume Resources: MtDB and Medicago.Org

    • Ernest F. Retzel, James E. Johnson, John A. Crow, Anne F. Lamblin, Charles E. Paule
    Pages 261-274

  14. BGI-RIS V2

    • Ximiao He, Jun Wang
    Pages 275-299

  15. GrainGenes

    • Helen O’Sullivan
    Pages 301-314

  16. Gramene

    • Doreen Ware
    Pages 315-329

  17. MaizeGDB

    • Carolyn J. Lawrence
    Pages 331-345

  18. BarleyBase/PLEXdb

    • Roger P. Wise, Rico A. Caldo, Lu Hong, Lishuang Shen, Ethalinda Cannon, Julie A. Dickerson
    Pages 347-363

  19. Reaping the Benefits of SAGE

    • Stephen J. Robinson, Justin D. Guenther, Christopher T. Lewis, Matthew G. Links, Isobel A.P. Parkin
    Pages 365-386

  20. Methods for Analysis of Gene Expression in Plants Using MPSS

    • Kan Nobuta, Kalyan Vemaraju, Blake C. Meyers
    Pages 387-407
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Keywords

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.

Editors and Affiliations

  • Primary Industries Research Victoria, Plant Genetics and Genomics,Victorian AgriBiosciences Centre, La Trobe University, Bundoora, Australia

    David Edwards

Bibliographic Information

  • Book Title: Plant Bioinformatics

  • Book Subtitle: Methods and Protocols

  • Editors: David Edwards

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-59745-535-0

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2007

  • Hardcover ISBN: 978-1-58829-653-5Published: 07 January 2008

  • Softcover ISBN: 978-1-61737-697-9Published: 19 November 2010

  • eBook ISBN: 978-1-59745-535-0Published: 03 February 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XV, 552

  • Number of Illustrations: 179 b/w illustrations

  • Topics: Plant Sciences, Bioinformatics

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