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Plant Bioinformatics - Methods and Protocols

Edited by D Edwards 
Springer  2007  



Hardcover  522 pp  ISBN 9781588296535      £106.00
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.

Of interest to plant biologists, geneticists, molecular and cellular biologists, computational biologists and bioinformaticians

Contents

  • The EMBL Nucleotide Sequence and Genome Reviews Databases
  • Using GenBank
  • A Collection of Plant-Specific Genomic Data and Resources at the National Center for Biotechnology Information
  • UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase
  • Plant Database Resources at The Institute for Genomic Research
  • MIPS Plant Genome Information Resources (PlantsDB)
  • HarvEST: an EST database-and viewing software
  • The TAIR Database
  • AtEnsembl - A post-genomic resource browser for Arabidopsis
  • Accessing integrated Brassica genetic and genomic data using the BASC server
  • Leveraging model legume information to find candidate genes for soybean Sudden Death Syndrome using the Legume Information System (LIS)
  • Legume resources: MtDB and medicago.org
  • BGI-RIS V2: Rice Information System at the Beijing Genomics Institute
  • GrainGenes: A Genomic Database for Triticeae and Avena
  • Gramene: A Resource for Comparative Grass Genomics
  • MaizeGDB: The Maize Genetics and Genomics Database
  • BarleyBase/PLEXdb: A Unified Expression Profiling Database for Plants and Plant Pathogens
  • Reaping the benefits of SAGE
  • Methods for analysis of gene expression in plants using MPSS
  • Metabolomics Data Analysis, Visualization, and Integration
  • KEGG Bioinformatics Resource for Plant Genomics Research
  • Using ICIS to Integrate Crop Phenotype Data from Different Sources
  • Automated discovery of Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers
  • Methods for Gene Ontology Annotation
  • Gene Structure Annotation at PlantGDB
  • An Introduction to BioPerl
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