1. Using GenBank Eric W. Sayers and Ilene Karsch-Mizrachi
2. UniProtKB/Swiss-Prot, The Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View Emmanuel Boutet, Damien Lieberherr, Michael Tognolli, Michel Schneider, Parit Bansal, Alan J. Bridge, Sylvain Poux, Lydie Bougueleret, and Ioannis Xenarios
3. KEGG Bioinformatics Resource for Plant Genomics and Metabolomics Minoru Kanehisa
4. Plant Pathway Databases Pankaj Jaiswal and Björn Usadel
5. The Plant Ontology: A Tool for Plant Genomics Laurel Cooper and Pankaj Jaiswal 6. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data Dan Bolser, Daniel M. Staines, Emily Pritchard, and Paul Kersey
7. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways Marcela Karey Monaco, Joshua Stein, Sharon Wei, Ken Youens-Clark, Pankaj Jaiswal, and Doreen Ware
8. PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes Manuel Spannagl, Kai Bader, Matthias Pfeifer, Thomas Nussbaumer, and Klaus FX Mayer
9. MaizeGDB: The Maize Genetics and Genomics Database Lisa Harper, Jack Gardiner, Carson Andorf, and Carolyn J. Lawrence
10. WheatGenome.info: A Resource for Wheat Genomics Resource Kaitao Lai
11. User Guidelines for the Brassica Database: BRAD Xiaobo Wang, Feng Cheng, and Xiaowu Wang
12. TAG Sequence Identification of Genomic Regions Using TAGdb Pradeep Ruperao
13. Short Read Alignment Using SOAP2 Bhavna Hurgobin
14. Tablet: Visualizing Next-Generation Sequence Assemblies and Mappings Iain Milne, Micha Bayer, Gordon Stephen, Linda Cardle, and David Marshall
15. Analysis of Genotyping-by-Sequencing (GBS) Data Sateesh Kagale, Chushin Koh, Wayne E. Clarke, Venkatesh Bollina, Isobel A.P. Parkin, and Andrew G. Sharpe
16. Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions and Improve Genome Assemblies Philipp Emanuel Bayer
17. Finding and Characterizing Repeats in Plant Genomes Jacques Nicolas, Pierre Peterlongo, and Sébastien Tempel
18. Analysis of RNA-Seq Data Using TopHat and Cufflinks Sreya Ghosh and Chon-Kit Kenneth Chan
The second edition of this volume focuses on applied bioinformatics with specific applications to crops and model plants. Plant Bioinformatics: Methods and Protocols is aimed at plant biologists who have an interest in, or requirement for, accessing and manipulating huge amounts of data being generated by high throughput technologies. This book would also be of interest to bioinformaticians and computer scientists who would benefit from an introduction to the different tools and systems available for plant research. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and software, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and thorough, Plant Bioinformatics: Methods and Protocols helps researchers with the increasing volume and diversity of data from different plants and also the integration of multiple diverse forms of data.