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TitlePlant Genomics Databases [electronic resource] : Methods and Protocols
Author edited by Aalt D.J van Dijk
ImprintNew York, NY : Springer New York : Imprint: Humana Press, 2017
Connect tohttp://dx.doi.org/10.1007/978-1-4939-6658-5
Descript XII, 336 p. 141 illus., 136 illus. in color. online resource

SUMMARY

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


CONTENT

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


Life sciences Plant science Botany Life Sciences Plant Sciences



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