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Plant Bioinformatics

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. David Edwards

    1. School of Biological Sciences, University of Western Australia, Perth, Australia

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  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2443)

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Table of contents (28 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Using GenBank and SRA

    • Eric W. Sayers, Chris O’Sullivan, Ilene Karsch-Mizrachi
    Pages 1-25

  3. Scripting Analyses of Genomes in Ensembl Plants

    • Bruno Contreras-Moreira, Guy Naamati, Marc Rosello, James E. Allen, Sarah E. Hunt, Matthieu Muffato et al.
    Pages 27-55Open Access

  4. CyVerse for Reproducible Research: RNA-Seq Analysis

    • Jason Williams
    Pages 57-79Open Access

  5. Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources

    • Sven Redsun, Sam Hokin, Connor T. Cameron, Alan M. Cleary, Joel Berendzen, Sudhansu Dash et al.
    Pages 81-100

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

    • Marcela Karey Tello-Ruiz, Pankaj Jaiswal, Doreen Ware
    Pages 101-131

  7. CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource

    • Mark Winfield, Paul Wilkinson, Amanda Burridge, Alexandra Allen, Jane Coghill, Christy Waterfall et al.
    Pages 133-146

  8. The Barley and Wheat Pan-Genomes

    • Nadia Kamal, Thomas Lux, Murukarthick Jayakodi, Georg Haberer, Heidrun Gundlach, Klaus F. X. Mayer et al.
    Pages 147-159

  9. Basics of Bash

    • Robyn Anderson
    Pages 161-180

  10. Pipeline Automation via Snakemake

    • Jakob Petereit
    Pages 181-196

  11. SciApps: An Automated Platform for Processing and Distribution of Plant Genomics Data

    • Liya Wang, Zhenyuan Lu, Peter Van Buren, Doreen Ware
    Pages 197-209

  12. Trimming and Validation of Illumina Short Reads Using Trimmomatic, Trinity Assembly, and Assessment of RNA-Seq Data

    • Steven O. Sewe, Gonçalo Silva, Paulo Sicat, Susan E. Seal, Paul Visendi
    Pages 211-232

  13. De Novo Assembly of Linked Reads Using Supernova 2.0

    • Paul Visendi
    Pages 233-243

  14. Applications of Optical Mapping for Plant Genome Assembly and Structural Variation Detection

    • Yuxuan Yuan
    Pages 245-257

  15. Making a Pangenome Using the Iterative Mapping Approach

    • Cassandria Tay Fernandez
    Pages 259-271

  16. Construction of Practical Haplotype Graph (PHG) with the Whole-Genome Sequence Data

    • Pradeep Ruperao, Prasad Gandham, Abhishek Rathore
    Pages 273-284

  17. Visualization Tools for Genomic Conservation

    • Venkat Bandi, Carl Gutwin, Jorge Núñez Siri, Eric Neufeld, Andrew Sharpe, Isobel Parkin
    Pages 285-308

  18. Annotation of Protein-Coding Genes in Plant Genomes

    • Bhavna Hurgobin
    Pages 309-326

  19. Finding and Characterizing Repeats in Plant Genomes

    • Jacques Nicolas, Sébastien Tempel, Anna-Sophie Fiston-Lavier, Emira Cherif
    Pages 327-385

  20. Gene Co-expression Network Analysis

    • Juan D. Montenegro
    Pages 387-404
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Keywords

About this book

This new edition focuses on applied bioinformatics with specific applications to crops, model and diverse plant species. The scope extends from the genome to the phenome and includes aspects of data management, analysis, visualization, and integration. The methods and approaches found within reflect the increasing use of high performance computing infrastructure to analyze and manage the enormous volume of data being generated by the latest high throughput technologies, the establishment and further maturation of major database systems and repositories, as well as the introduction of new approaches such as machine learning. Written for the highly successful Methods in Molecular Biology series, the chapters include the kind of detailed implementation advice that leads to successful research results. 

Authoritative and up-to-date, Plant Bioinformatics: Methods and Protocols, Third Edition will aid researchers exploring the broad comparison of speciesthat will drive future plant research, crop breeding, and bioinformatics developments that allow us to understand and manipulate the heritable differences between individuals and populations. 


Chapters 2, 3, and 26 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Editors and Affiliations

  • School of Biological Sciences, 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/10.1007/978-1-0716-2067-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-2066-3Published: 17 January 2022

  • Softcover ISBN: 978-1-0716-2069-4Published: 18 January 2023

  • eBook ISBN: 978-1-0716-2067-0Published: 16 January 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 3

  • Number of Pages: XIV, 544

  • Number of Illustrations: 8 b/w illustrations, 108 illustrations in colour

  • Topics: Bioinformatics, Plant Sciences

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