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Plant Genomics Databases

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Aalt D.J van Dijk

    1. PRI Bioscience, Biometris and Bioinformatics, Wageningen University & Research Wageningen, Wageningen, The Netherlands

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains keynotes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1533)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data

    • Dan M. Bolser, Daniel M. Staines, Emily Perry, Paul J. Kersey
    Pages 1-31

  3. PGSB/MIPS PlantsDB Database Framework for the Integration and Analysis of Plant Genome Data

    • Manuel Spannagl, Thomas Nussbaumer, Kai Bader, Heidrun Gundlach, Klaus F. X. Mayer
    Pages 33-44

  4. Plant Genome DataBase Japan (PGDBj)

    • Akihiro Nakaya, Hisako Ichihara, Erika Asamizu, Sachiko Shirasawa, Yasukazu Nakamura, Satoshi Tabata et al.
    Pages 45-77

  5. FLAGdb++: A Bioinformatic Environment to Study and Compare Plant Genomes

    • Jean Philippe Tamby, Véronique Brunaud
    Pages 79-101

  6. Mining Plant Genomic and Genetic Data Using the GnpIS Information System

    • A.-F. Adam-Blondon, M. Alaux, S. Durand, T. Letellier, G. Merceron, N. Mohellibi et al.
    Pages 103-117

  7. The Bio-Analytic Resource for Plant Biology

    • Jamie Waese, Nicholas J. Provart
    Pages 119-148

  8. The Evolution of Soybean Knowledge Base (SoyKB)

    • Trupti Joshi, Jiaojiao Wang, Hongxin Zhang, Shiyuan Chen, Shuai Zeng, Bowei Xu et al.
    Pages 149-159

  9. Using TropGeneDB: A Database Containing Data on Molecular Markers, QTLs, Maps, Genotypes, and Phenotypes for Tropical Crops

    • Manuel Ruiz, Guilhem Sempéré, Chantal Hamelin
    Pages 161-172

  10. Species-Specific Genome Sequence Databases: A Practical Review

    • A. D. J. van Dijk
    Pages 173-181

  11. A Guide to the PLAZA 3.0 Plant Comparative Genomic Database

    • Klaas Vandepoele
    Pages 183-200

  12. Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0

    • Michiel Van Bel, Frederik Coppens
    Pages 201-212

  13. PlaNet: Comparative Co-Expression Network Analyses for Plants

    • Sebastian Proost, Marek Mutwil
    Pages 213-227

  14. Practical Utilization of OryzaExpress and Plant Omics Data Center Databases to Explore Gene Expression Networks in Oryza Sativa and Other Plant Species

    • Toru Kudo, Shin Terashima, Yuno Takaki, Yukino Nakamura, Masaaki Kobayashi, Kentaro Yano
    Pages 229-240

  15. Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study

    • Sushma Naithani, Pankaj Jaiswal
    Pages 241-256

  16. CSGRqtl: A Comparative Quantitative Trait Locus Database for Saccharinae Grasses

    • Dong Zhang, Andrew H. Paterson
    Pages 257-266

  17. Plant Genome Duplication Database

    • Tae-Ho Lee, Junah Kim, Jon S. Robertson, Andrew H. Paterson
    Pages 267-277

  18. Variant Effect Prediction Analysis Using Resources Available at Gramene Database

    • Sushma Naithani, Matthew Geniza, Pankaj Jaiswal
    Pages 279-297

  19. Plant Promoter Database (PPDB)

    • Kazutaka Kusunoki, Yoshiharu Y. Yamamoto
    Pages 299-314

  20. Construction of the Leaf Senescence Database and Functional Assessment of Senescence-Associated Genes

    • Zhonghai Li, Yi Zhao, Xiaochuan Liu, Zhiqiang Jiang, Jinying Peng, Jinpu Jin et al.
    Pages 315-333
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Keywords

About this book

This volume introduces databases containing the results from the recent revolution in sequencing technologies. Chapters in Plant Genomics Databases: Methods and Protocols describe database content, as well as typical use-cases. Some chapters explore databases that primarily present genome sequences focusing on one or a few related species, while others include additional datatypes and/or data from various plant species. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.


Cutting-edge and comprehensive, Plant Genomics Databases: Methods and Protocols is a valuable resource for providing clear guidance in accessing an important collection of plant databases that can be used to add biological value to genomic data.

Editors and Affiliations

  • PRI Bioscience, Biometris and Bioinformatics, Wageningen University & Research Wageningen, Wageningen, The Netherlands

    Aalt D.J van Dijk

Bibliographic Information

  • Book Title: Plant Genomics Databases

  • Book Subtitle: Methods and Protocols

  • Editors: Aalt D.J van Dijk

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-6658-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2017

  • Hardcover ISBN: 978-1-4939-6656-1Published: 17 December 2016

  • Softcover ISBN: 978-1-4939-8263-9Published: 07 July 2018

  • eBook ISBN: 978-1-4939-6658-5Published: 16 December 2016

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 336

  • Number of Illustrations: 5 b/w illustrations, 136 illustrations in colour

  • Topics: Plant Sciences

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