Plant Bioinformatics

Using GenBank.- UniProtKB/Swiss-Prot, The Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View.- KEGG Bioinformatics Resource for Plant Genomics and Metabolomics.- Plant Pathway Databases.- The Plant Ontology: A Tool for Plant Genomics.- Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.- Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.- PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes.- MaizeGDB: The Maize Genetics and Genomics Database.- WheatGenome.info: A Resource for Wheat Genomics Resource.- User Guidelines for the Brassica Database: BRAD.- TAG Sequence Identification of Genomic Regions Using TAGdb.- Short Read Alignment Using SOAP2.- Tablet: Visualizing Next-Generation Sequence Assemblies and Mappings.- Analysis of Genotyping-by-Sequencing (GBS) Data.- Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions and Improve Genome Assemblies.- Finding and Characterizing Repeats in Plant Genomes.- Analysis of RNA-Seq Data Using TopHat and Cufflinks.