Plant Bioinformatics: Methods and Protocols / Edition 1

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Bioinformatics is a rapidly developing field. Data volumes continue to grow and there is an increasing breadth of available data, including sequence, gene expression, protein, metabolite and phenotypic data. Novel databases are being developed for specific species or experiment types. These databases and tools may greatly assist in the application of plant biotechnology, though they require a basic set of skills to identify and utilize the most appropriate resource. This book aims to assist research scientists in choosing the most applicable database or bioinformatics tools to aid and promote their research in plant biotechnology. Chapters include practical examples and highlight common problems encountered in bioinformatics analysis. Further chapters are aimed at researchers developing bioinformatics databases and tools, detailing commonly applied database formats and biology-focused scripting languages. These will provide both beginner and experienced bioinformatics researchers with the necessary skills to develop and apply bioinformatics tools for their specialist area of plant research.

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Product Details

  • ISBN-13: 9781588296535
  • Publisher: Springer-Verlag New York, LLC
  • Publication date: 1/28/2008
  • Series: Methods in Molecular Biology Series, #406
  • Edition description: 2007
  • Edition number: 1
  • Pages: 552
  • Product dimensions: 6.05 (w) x 9.27 (h) x 1.44 (d)

Table of Contents

Preface     v
Contributors     xi
The EMBL Nucleotide Sequence and Genome Reviews Databases   Peter Sterk   Tamara Kulikova   Paul Kersey   Rolf Apweiler     1
Using GenBank   David Wheeler     23
A Collection of Plant-Specific Genomic Data and Resources at NCBI   Tatiana Tatusova   Brian Smith-White   James Ostell     61
UniProtKB/Swiss-Prot   Emmanuel Boutet   Damien Lieberherr   Michael Tognolli   Michel Schneider   Amos Bairoch     89
Plant Database Resources at The Institute for Genomic Research   Agnes P. Chan   Pablo D. Rabinowicz   John Quackenbush   C. Robin Buell   Chris D. Town     113
MIPS Plant Genome Information Resources   Manuel Spannagl   Georg Haberer   Rebecca Ernst   Heiko Schoof   Klaus F. X. Mayer     137
HarvEST   Timothy J. Close   Steve Wanamaker   Mikeal L. Roose   Matthew Lyon     161
The TAIR Database   Rebecca L. Poole     179
AtEnsEMBL   Nick James   Neil Graham   Debbie Clements   Beatrice Schildknecht   Sean May     213
Accessing Integrated Brassica Genetic and Genomic Data Using the BASC Server   Christopher G. Love   David Edwards     229
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
Legume Resources: MtDB and Medicago.Org   Ernest F. Retzel   James E. Johnson   John A. Crow   Anne F. Lamblin   Charles E. Paule     261
BGI-RIS V2   Ximiao He   Jun Wang     275
GrainGenes   Helen O'Sullivan     301
Gramene   Doreen Ware     315
MaizeGDB   Carolyn J. Lawrence     331
BarleyBase/PLEXdb   Roger P. Wise   Rico A. Caldo   Lu Hong   Lishuang Shen   Ethalinda Cannon   Julie A. Dickerson     347
Reaping the Benefits of SAGE   Stephen J. Robinson   Justin D. Guenther   Christopher T. Lewis   Matthew G. Links   Isobel A.P. Parkin     365
Methods for Analysis of Gene Expression in Plants Using MPSS   Kan Nobuta   Kalyan Vemaraju   Blake C. Meyers     387
Metabolomics Data Analysis, Visualization, and Integration   Lloyd W. Sumner   Ewa Urbanczyk-Wochniak   Corey D. Broeckling     409
KEGG Bioinformatics Resource for Plant Genomics Research   Ali Masoudi-Nejad   Susumu Goto   Takashi R. Endo   Minoru Kanehisa     437
International Crop Information System for Germplasm Data Management   Arllet Portugal   Ranjan Balachandra   Thomas Metz   Richard Bruskiewich   Graham McLaren     459
Automated Discovery of Single Nucleotide Polymorphism and Simple Sequence Repeat Molecular Genetic Markers   Jacqueline Batley   Erica Jewell   David Edwards     473
Methods for Gene Ontology Annotation   Emily Dimmer   Tanya Z. Berardini   Daniel Barrell   Evelyn Camon     495
Gene Structure Annotation at PlantGDB   Volker Brendel     521
An Introduction to BioPerl   Jason E. Stajich     535
Index     549
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