Plant Genomics Databases: Methods and Protocols

by Aalt D.J van Dijk (Editor)

Overview

This volume introduces databases containing the results from the recent revolution in sequencing technologies. Chapters in Plant Genomics Databases: Methods and Prools 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 prools, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and comprehensive, Plant Genomics Databases: Methods and Prools 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.

Product Details

ISBN-13:	9781493966561
Publisher:	Springer New York
Publication date:	12/17/2016
Series:	Methods in Molecular Biology , #1533
Edition description:	1st ed. 2017
Pages:	336
Product dimensions:	7.01(w) x 10.00(h) x (d)

Table of Contents

Ensembl Plants: Integrating Tools for Visualizing, Mining and Analyzing Plant Genomics Data.- PGSB/MIPS PlantsDB Database Framework for the Integration and Analysis of Plant Genome Data.- Plant Genome DataBase Japan (PGDBj).- FLAGdb++: A Bioinformatic Environment to Study and Compare Plant Genomes.- Mining Plant Genomic and Genetic Data Using the GnpIS Information System.- The Bio-Analytic Resource for Plant Biology.- The Evolution of Soybean Knowledge Base (SoyKB).- Using TropGeneDB: a Database Containing Data on Molecular Markers, QTLs, Maps, Genotypes, and Phenotypes for Tropical Crops.- Species-Specific Genome Sequence Databases: A Practical Review.- A Guide to the PLAZA 3.0 Plant Comparative Genomics Database.- Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0.- PlaNet: Comparative Co-Expression Network Analyses for Plants.- Practical Utilization of OryzaExpress and Plant Omics Data Center Databases to Explore Gene Expression Networks in Oryza sativa and Other Plant Species.- Pathway Analysis and Omics Data Visualization using Pathway Genome Databases: FragariaCyc, A Case Study.- CSGRqtl: A Comparative Quantitative Trait Locus Database for Saccharinae Grasses.- Plant Genome Duplication Database.- Variant Effect Prediction Analysis using Resources Available at Gramene Database.- Plant Promoter Database.- Construction of the Leaf Senescence Database and Functional Assessment of Senescence-Associated Genes.