Description
Book SynopsisThe 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 a
Table of Contents
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
