Plant Bioinformatics Methods and Protocols

About this book

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.

Contents

Plant Bioinformatics 1 The EMBL Nucleotide Sequence and Genome Reviews Databases 2 Using GenBank 3 A Collection of Plant-Specific Genomic Data and Resources at the National Center for Biotechnology Information 4 UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase 5 Plant Database Resources at The Institute for Genomic Research 6 MIPS Plant Genome Information Resources (PlantsDB) 7 HarvEST: an EST database-and viewing software 8 The TAIR Database 9 AtEnsembl - A post-genomic resource browser for Arabidopsis 10 Accessing integrated Brassica genetic and genomic data using the BASC server 11 Leveraging model legume information to find candidate genes for soybean Sudden Death Syndrome using the Legume Information System (LIS) 12 Legume resources: MtDB and medicago.org 13 BGI-RIS V2: Rice Information System at the Beijing Genomics Institute 14 GrainGenes: A Genomic Database for Triticeae and Avena 15 Gramene: A Resource for Comparative Grass Genomics 16 MaizeGDB: The Maize Genetics and Genomics Database 17 BarleyBase/PLEXdb: A Unified Expression Profiling Database for Plants and Plant Pathogens 18 Reaping the benefits of SAGE 19 Methods for analysis of gene expression in plants using MPSS 20 Metabolomics Data Analysis, Visualization, and Integration 21 KEGG Bioinformatics Resource for Plant Genomics Research 22 Using ICIS to Integrate Crop Phenotype Data from Different Sources 23 Automated discovery of Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers 24 Methods for Gene Ontology Annotation 25 Gene Structure Annotation at PlantGDB 26 An Introduction to BioPerl

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