Plant Bioinformatics

1. Using GenBankEric W. Sayers and Ilene Karsch-Mizrachi2. UniProtKB/Swiss-Prot, The Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry ViewEmmanuel Boutet, Damien Lieberherr, Michael Tognolli, Michel Schneider, Parit Bansal, Alan J. Bridge, Sylvain Poux, Lydie Bougueleret, and Ioannis Xenarios3. KEGG Bioinformatics Resource for Plant Genomics and MetabolomicsMinoru Kanehisa4. Plant Pathway DatabasesPankaj Jaiswal and Bjorn Usadel5. The Plant Ontology: A Tool for Plant GenomicsLaurel Cooper and Pankaj Jaiswal6. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics DataDan Bolser, Daniel M. Staines, Emily Pritchard, and Paul Kersey7. Gramene: A Resource for Comparative Analysis of Plants Genomes and PathwaysMarcela Karey Monaco, Joshua Stein, Sharon Wei, Ken Youens-Clark, Pankaj Jaiswal, and Doreen Ware8. PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass GenomesManuel Spannagl, Kai Bader, Matthias Pfeifer, Thomas Nussbaumer, and Klaus FX Mayer9. MaizeGDB: The Maize Genetics and Genomics DatabaseLisa Harper, Jack Gardiner, Carson Andorf, and Carolyn J. Lawrence10. WheatGenome.info: A Resource for Wheat Genomics ResourceKaitao Lai11. User Guidelines for the Brassica Database: BRADXiaobo Wang, Feng Cheng, and Xiaowu Wang12. TAG Sequence Identification of Genomic Regions Using TAGdbPradeep Ruperao13. Short Read Alignment Using SOAP2Bhavna Hurgobin14. Tablet: Visualizing Next-Generation Sequence Assemblies and MappingsIain Milne, Micha Bayer, Gordon Stephen, Linda Cardle, and David Marshall15. Analysis of Genotyping-by-Sequencing (GBS) DataSateesh Kagale, Chushin Koh, Wayne E. Clarke, Venkatesh Bollina, Isobel A.P. Parkin, and Andrew G. Sharpe16. Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions and Improve Genome AssembliesPhilipp Emanuel Bayer17. Finding and Characterizing Repeats in Plant GenomesJacques Nicolas, Pierre Peterlongo, and Sebastien Tempel18. Analysis of RNA-Seq Data Using TopHat and Cufflinks Sreya Ghosh and Chon-Kit Kenneth Chan