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Plant Genomics Databases

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Cover of 'Plant Genomics Databases'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data.
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    Chapter 2 PGSB/MIPS PlantsDB Database Framework for the Integration and Analysis of Plant Genome Data.
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    Chapter 3 Plant Genome DataBase Japan (PGDBj).
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    Chapter 4 FLAGdb(++): A Bioinformatic Environment to Study and Compare Plant Genomes.
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    Chapter 5 Mining Plant Genomic and Genetic Data Using the GnpIS Information System.
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    Chapter 6 The Bio-Analytic Resource for Plant Biology.
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    Chapter 7 The Evolution of Soybean Knowledge Base (SoyKB).
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    Chapter 8 Using TropGeneDB: A Database Containing Data on Molecular Markers, QTLs, Maps, Genotypes, and Phenotypes for Tropical Crops.
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    Chapter 9 Species-Specific Genome Sequence Databases: A Practical Review.
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    Chapter 10 A Guide to the PLAZA 3.0 Plant Comparative Genomic Database.
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    Chapter 11 Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0.
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    Chapter 12 PlaNet: Comparative Co-Expression Network Analyses for Plants.
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    Chapter 13 Practical Utilization of OryzaExpress and Plant Omics Data Center Databases to Explore Gene Expression Networks in Oryza Sativa and Other Plant Species.
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    Chapter 14 Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study.
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    Chapter 15 CSGRqtl: A Comparative Quantitative Trait Locus Database for Saccharinae Grasses.
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    Chapter 16 Plant Genome Duplication Database.
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    Chapter 17 Variant Effect Prediction Analysis Using Resources Available at Gramene Database.
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    Chapter 18 Plant Promoter Database (PPDB).
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    Chapter 19 Construction of the Leaf Senescence Database and Functional Assessment of Senescence-Associated Genes.
Attention for Chapter 9: Species-Specific Genome Sequence Databases: A Practical Review.
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Chapter title
Species-Specific Genome Sequence Databases: A Practical Review.
Chapter number 9
Book title
Plant Genomics Databases
Published in
Methods in molecular biology, January 2017
DOI 10.1007/978-1-4939-6658-5_9
Pubmed ID
Book ISBNs
978-1-4939-6656-1, 978-1-4939-6658-5
Authors

A. D. J. van Dijk

Editors

Aalt D.J van Dijk

Abstract

This chapter presents a use case illustrating the search for homologues of a known protein in species-specific genome sequence databases. The results from different species-specific resources are compared to each other and to results obtained from a more general genome sequence database (Phytozome). Various options and settings relevant when searching these databases are discussed. For example, it is shown how the choice of reference sequence set in a given database influences the results one obtains. The provided examples illustrate some problems and pitfalls related to interpreting results obtained from species-specific genome sequence databases.

Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 46 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 2%
Unknown 45 98%

Demographic breakdown

Readers by professional status Count As %
Researcher 10 22%
Student > Ph. D. Student 9 20%
Student > Master 5 11%
Student > Doctoral Student 4 9%
Student > Bachelor 3 7%
Other 7 15%
Unknown 8 17%
Readers by discipline Count As %
Agricultural and Biological Sciences 24 52%
Biochemistry, Genetics and Molecular Biology 9 20%
Nursing and Health Professions 1 2%
Medicine and Dentistry 1 2%
Chemistry 1 2%
Other 0 0%
Unknown 10 22%