Plant bioinformatics : methods and protocols

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.

Peter Sterk and Tamara Kulikova and Paul Kersey and Rolf ApweilerDavid WheelerTatiana Tatusova and Brian Smith-White and James OstellEmmanuel Boutet and Damien Lieberherr and Michael Tognolli and Michel Schneider and Amos BairochAgnes P. Chan and Pablo D. Rabinowicz and John Quackenbush and C. Robin Buell and Chris D. TownManuel Spannagl and Georg Haberer and Rebecca Ernst and Heiko Schoof and Klaus F. X. MayerTimothy J. Close and Steve Wanamaker and Mikeal L. Roose and Matthew LyonRebecca L. PooleNick James and Neil Graham and Debbie Clements and Beatrice Schildknecht and Sean MayChristopher G. Love and David EdwardsMichael D. Gonzales and Kamal Gajendran and Andrew D. Farmer and Eric Archuleta and William D. BeavisErnest F. Retzel and James E. Johnson and John A. Crow and Anne F. Lamblin and Charles E. PauleXimiao He and Jun WangHelen O'SullivanDoreen WareCarolyn J. LawrenceRoger P. Wise and Rico A. Caldo and Lu Hong and Lishuang Shen and Ethalinda Cannon and Julie A. DickersonStephen J. Robinson and Justin D. Guenther and Christopher T. Lewis and Matthew G. Links and Isobel A.P. ParkinKan Nobuta and Kalyan Vemaraju and Blake C. MeyersLloyd W. Sumner and Ewa Urbanczyk-Wochniak and Corey D. BroecklingAli Masoudi-Nejad and Susumu Goto and Takashi R. Endo and Minoru KanehisaArllet Portugal and Ranjan Balachandra and Thomas Metz and Richard Bruskiewich and Graham McLarenJacqueline Batley and Erica Jewell and David EdwardsEmily Dimmer and Tanya Z. Berardini and Daniel Barrell and Evelyn CamonVolker BrendelJason E. Stajich

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

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