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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.
List of contents
The EMBL Nucleotide Sequence and Genome Reviews Databases.- Using GenBank.- A Collection of Plant-Specific Genomic Data and Resources at NCBI.- UniProtKB/Swiss-Prot.- Plant Database Resources at The Institute for Genomic Research.- MIPS Plant Genome Information Resources.- HarvEST.- The TAIR Database.- AtEnsEMBL.- Accessing Integrated Brassica.- Leveraging Model Legume Information to Find Candidate Genes for Soybean Sudden Death Syndrome Using the Legume Information System.- Legume Resources: MtDB and Medicago.Org.- BGI-RIS V2.- GrainGenes.- Gramene.- MaizeGDB.- BarleyBase/PLEXdb.- 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.- International Crop Information System for Germplasm Data Management.- Automated Discovery of Single Nucleotide Polymorphism and Simple Sequence Repeat Molecular Genetic Markers.- Methods for Gene Ontology Annotation.- Gene Structure Annotation at PlantGDB.- An Introduction to BioPerl.
About the author
David Edwards researches Statistical Bioinformatics at Aarhus University's Department of Molecular Biology and Genetics.
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 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.
