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Plant Bioinformatics

Methods and Protocols

  • Book
  • © 2016

Overview

Editors:
  1. David Edwards

    1. School of Plant Biology, University of Western Australia, Perth, Australia

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  • 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 1374)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xi
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  2. Using GenBank

    • Eric W. Sayers, Ilene Karsch-Mizrachi
    Pages 1-22

  3. UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View

    • Emmanuel Boutet, Damien Lieberherr, Michael Tognolli, Michel Schneider, Parit Bansal, Alan J. Bridge et al.
    Pages 23-54

  4. KEGG Bioinformatics Resource for Plant Genomics and Metabolomics

    • Minoru Kanehisa
    Pages 55-70

  5. Plant Pathway Databases

    • Pankaj Jaiswal, Björn Usadel
    Pages 71-87

  6. The Plant Ontology: A Tool for Plant Genomics

    • Laurel Cooper, Pankaj Jaiswal
    Pages 89-114

  7. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data

    • Dan Bolser, Daniel M. Staines, Emily Pritchard, Paul Kersey
    Pages 115-140

  8. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways

    • Marcela Karey Tello-Ruiz, Joshua Stein, Sharon Wei, Ken Youens-Clark, Pankaj Jaiswal, Doreen Ware
    Pages 141-163

  9. PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes

    • Manuel Spannagl, Kai Bader, Matthias Pfeifer, Thomas Nussbaumer, Klaus F. X. Mayer
    Pages 165-186

  10. MaizeGDB: The Maize Genetics and Genomics Database

    • Lisa Harper, Jack Gardiner, Carson Andorf, Carolyn J. Lawrence
    Pages 187-202

  11. WheatGenome.info: A Resource for Wheat Genomics Resource

    • Kaitao Lai
    Pages 203-213

  12. User Guidelines for the Brassica Database: BRAD

    • Xiaobo Wang, Feng Cheng, Xiaowu Wang
    Pages 215-231

  13. TAG Sequence Identification of Genomic Regions Using TAGdb

    • Pradeep Ruperao
    Pages 233-240

  14. Short Read Alignment Using SOAP2

    • Bhavna Hurgobin
    Pages 241-252

  15. Tablet: Visualizing Next-Generation Sequence Assemblies and Mappings

    • Iain Milne, Micha Bayer, Gordon Stephen, Linda Cardle, David Marshall
    Pages 253-268

  16. Analysis of Genotyping-by-Sequencing (GBS) Data

    • Sateesh Kagale, Chushin Koh, Wayne E. Clarke, Venkatesh Bollina, Isobel A. P. Parkin, Andrew G. Sharpe
    Pages 269-284

  17. Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies

    • Philipp Emanuel Bayer
    Pages 285-292

  18. Finding and Characterizing Repeats in Plant Genomes

    • Jacques Nicolas, Pierre Peterlongo, Sébastien Tempel
    Pages 293-337

  19. Analysis of RNA-Seq Data Using TopHat and Cufflinks

    • Sreya Ghosh, Chon-Kit Kenneth Chan
    Pages 339-361

  20. Back Matter

    Pages 363-365
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Keywords

About this book

The second edition of this volume focuses on applied bioinformatics with specific applications to crops and model plants. Plant Bioinformatics: Methods and Protocols is aimed at plant biologists who have an interest in, or requirement for, accessing and manipulating huge amounts of data being generated by high throughput technologies. This book would also be of interest to bioinformaticians and computer scientists who would benefit from an introduction to the different tools and systems available for plant research. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and software, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and thorough, Plant Bioinformatics: Methods and Protocols helps researchers with the increasing volume and diversity of data from different plants and also the integration of multiple diverse forms of data.

Editors and Affiliations

  • School of Plant Biology, University of Western Australia, Perth, 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/10.1007/978-1-4939-3167-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2016

  • Hardcover ISBN: 978-1-4939-3166-8Published: 03 November 2015

  • Softcover ISBN: 978-1-4939-4732-4Published: 23 August 2016

  • eBook ISBN: 978-1-4939-3167-5Published: 30 October 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XI, 365

  • Number of Illustrations: 12 b/w illustrations, 116 illustrations in colour

  • Topics: Plant Sciences

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