"Plant Bioinformatics"

Methods and Protocols

edited by Edwards, David

Springer, 2008, 640 pages. $139.00 + shipping ($8.00, U.S. or $15.00 Elsewhere)

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.

Contents:

Plant Bioinformatics

1 The EMBL Nucleotide Sequence and Genome Reviews Databases

2 Using GenBank

3 A Collection of Plant-Specific Genomic Data and Resources at the National Center for Biotechnology Information

4 UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase

5 Plant Database Resources at The Institute for Genomic Research

6 MIPS Plant Genome Information Resources (PlantsDB)

7 HarvEST: an EST database-and viewing software

8 The TAIR Database

9 AtEnsembl - A post-genomic resource browser for Arabidopsis

10 Accessing integrated Brassica genetic and genomic data using the BASC server

11 Leveraging model legume information to find candidate genes for soybean Sudden Death Syndrome using the Legume Information System (LIS)

12 Legume resources: MtDB and medicago.org

13 BGI-RIS V2: Rice Information System at the Beijing Genomics Institute

14 GrainGenes: A Genomic Database for Triticeae and Avena

15 Gramene: A Resource for Comparative Grass Genomics

16 MaizeGDB: The Maize Genetics and Genomics Database

17 BarleyBase/PLEXdb: A Unified Expression Profiling Database for Plants and Plant Pathogens

18 Reaping the benefits of SAGE

19 Methods for analysis of gene expression in plants using MPSS

20 Metabolomics Data Analysis, Visualization, and Integration

21 KEGG Bioinformatics Resource for Plant Genomics Research

22 Using ICIS to Integrate Crop Phenotype Data from Different Sources

23 Automated discovery of Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers

24 Methods for Gene Ontology Annotation

25 Gene Structure Annotation at PlantGDB

26 An Introduction to BioPerl

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