Plant Bioinformatics

Methods and Protocols

By: David Edwards (Editor)

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Hardcover | 11 February 2008

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572 Pages

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24.13 x 16.51 x 3.18

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Bioinformatics is a new and rapidly evolving field of research that is being driven by the development and application of various 'omics technologies. Plant Bioinformatics focuses on applied bioinformatics with specific applications to crops and model plants. Chapters in this new volume are aimed at researchers developing bioinformatics databases and tools, detailing commonly applied database formats and biology-focused scripting languages. These will provide both beginners and experienced bioinformatics researchers with the necessary skills to develop and apply bioinformatics tools for their specialist area of plant research. Each chapter includes practical examples and highlight common problems encountered in bioinformatics analysis. Protocols in this volume detail EMBL Nucleotide Sequence, TAIR database, VarvEST, MIPS, BGI-RIS V2, BarleyBase/PLEXdb, SAGE, KEGG, and more. Plant biologists who have an interest in or requirement for the accessing and manipulation of the huge amount of data being generated by high throughput technologies will find this new volume to be an immeasurable aid in their research.

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Preface	p. v
Contributors	p. xi
The EMBL Nucleotide Sequence and Genome Reviews Databases	p. 1
Using GenBank	p. 23
A Collection of Plant-Specific Genomic Data and Resources at NCBI	p. 61
UniProtKB/Swiss-Prot	p. 89
Plant Database Resources at The Institute for Genomic Research	p. 113
MIPS Plant Genome Information Resources	p. 137
HarvEST	p. 161
The TAIR Database	p. 179
AtEnsEMBL	p. 213
Accessing Integrated Brassica Genetic and Genomic Data Using the BASC Server	p. 229
Leveraging Model Legume Information to Find Candidate Genes for Soybean Sudden Death Syndrome Using the Legume Information System	p. 245
Legume Resources: MtDB and Medicago.Org	p. 261
BGI-RIS V2	p. 275
GrainGenes	p. 301
Gramene	p. 315
MaizeGDB	p. 331
BarleyBase/PLEXdb	p. 347
Reaping the Benefits of SAGE	p. 365
Methods for Analysis of Gene Expression in Plants Using MPSS	p. 387
Metabolomics Data Analysis, Visualization, and Integration	p. 409
KEGG Bioinformatics Resource for Plant Genomics Research	p. 437
International Crop Information System for Germplasm Data Management	p. 459
Automated Discovery of Single Nucleotide Polymorphism and Simple Sequence Repeat Molecular Genetic Markers	p. 473
Methods for Gene Ontology Annotation	p. 495
Gene Structure Annotation at PlantGDB	p. 521
An Introduction to BioPerl	p. 535
Index	p. 549
Table of Contents provided by Ingram. All Rights Reserved.

Plant Bioinformatics

Methods and Protocols

At a Glance

Hardcover

Shipping

How to return your order

Defective items

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