Plant bioinformatics : methods and protocols / edited by David Edwards.

Format:

Book

Contributor:

Edwards, David, 1967-

Series:

Methods in molecular biology (Clifton, N.J.) ; 406.

Methods in molecular biology ; 406

Language:

English

Subjects (All):

Bioinformatics.

Plant biotechnology.

Sequence Analysis--methods.

Computational Biology--methods.

Databases, Genetic.

Biotechnology.

Medical Subjects:

Sequence Analysis--methods.

Computational Biology--methods.

Databases, Genetic.

Biotechnology.

Physical Description:

xv, 552 pages : illustrations ; 24 cm.

Place of Publication:

Totowa, N.J. : Humana, 2007.

Summary:

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 will provide both beginners and experienced researchers with the necessary skills to apply bioinformatics tools for their specialist area, and provide bioinformaticians and computer scientists with an introduction to the different tools and systems available for plant research. Each chapter includes practical examples and highlights common problems encountered in bioinformatics analysis. Protocols in this volume detail EMBL, TAIR, HarvEST, Graingenes, Gramene, BGI-RIS V2, AtEnsEMBL, MaizeGDB, BarleyBase/PLEXdb, SAGE, MPSS, KEGG, BioPerl 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:

1 The EMBL Nucleotide Sequence and Genome Reviews Databases / Peter Sterk, Tamara Kulikova, Paul Kersey, Rolf Apweiler 1

2 Using GenBank / David Wheeler 23

3 A Collection of Plant-Specific Genomic Data and Resources at NCBI / Tatiana Tatusova, Brian Smith-White, James Ostell 61

4 UniProtKB/Swiss-Prot / Emmanuel Boutet, Damien Lieberherr, Michael Tognolli, Michel Schneider, Amos Bairoch 89

5 Plant Database Resources at The Institute for Genomic Research / Agnes P. Chan, Pablo D. Rabinowicz, John Quackenbush, C. Robin Buell, Chris D. Town 113

6 MIPS Plant Genome Information Resources / Manuel Spannagl, Georg Haberer, Rebecca Ernst, Heiko Schoof, Klaus F. X. Mayer 137

7 HarvEST / Timothy J. Close, Steve Wanamaker, Mikeal L. Roose, Matthew Lyon 161

8 The TAIR Database / Rebecca L. Poole 179

9 AtEnsEMBL / Nick James, Neil Graham, Debbie Clements, Beatrice Schildknecht, Sean May 213

10 Accessing Integrated Brassica Genetic and Genomic Data Using the BASC Server / Christopher G. Love, David Edwards 229

11 Leveraging Model Legume Information to Find Candidate Genes for Soybean Sudden Death Syndrome Using the Legume Information System / Michael D. Gonzales, Kamal Gajendran, Andrew D. Farmer, Eric Archuleta, William D. Beavis 245

12 Legume Resources: MtDB and Medicago.Org / Ernest F. Retzel, James E. Johnson, John A. Crow, Anne F. Lamblin, Charles E. Paule 261

13 BGI-RIS V2 / Ximiao He, Jun Wang 275

14 GrainGenes / Helen O'Sullivan 301

15 Gramene / Doreen Ware 315

16 MaizeGDB / Carolyn J. Lawrence 331

17 BarleyBase/PLEXdb / Roger P. Wise, Rico A. Caldo, Lu Hong, Lishuang Shen, Ethalinda Cannon, Julie A. Dickerson 347

18 Reaping the Benefits of SAGE / Stephen J. Robinson, Justin D. Guenther, Christopher T. Lewis, Matthew G. Links, Isobel A.P. Parkin 365

19 Methods for Analysis of Gene Expression in Plants Using MPSS / Kan Nobuta, Kalyan Vemaraju, Blake C. Meyers 387

20 Metabolomics Data Analysis, Visualization, and Integration / Lloyd W. Sumner, Ewa Urbanczyk-Wochniak, Corey D. Broeckling 409

21 KEGG Bioinformatics Resource for Plant Genomics Research / Ali Masoudi-Nejad, Susumu Goto, Takashi R. Endo, Minoru Kanehisa 437

22 International Crop Information System for Germplasm Data Management / Arllet Portugal, Ranjan Balachandra, Thomas Metz, Richard Bruskiewich, Graham McLaren 459

23 Automated Discovery of Single Nucleotide Polymorphism and Simple Sequence Repeat Molecular Genetic Markers / Jacqueline Batley, Erica Jewell, David Edwards 473

24 Methods for Gene Ontology Annotation / Emily Dimmer, Tanya Z. Berardini, Daniel Barrell, Evelyn Camon 495

25 Gene Structure Annotation at PlantGDB / Volker Brendel 521

26 An Introduction to BioPerl / Jason E. Stajich 535.

Notes:

Includes bibliographical references and index.

ISBN:

9781588296535

1588296539

OCLC:

123798707