Plant Bioinformatics Methods and Protocols

This new edition focuses on applied bioinformatics with specific applications to crops, model and diverse plant species. The scope extends from the genome to the phenome and includes aspects of data management, analysis, visualization, and integration. The methods and approaches found within reflect the increasing use of high performance computing infrastructure to analyze and manage the enormous volume of data being generated by the latest high throughput technologies, the establishment and further maturation of major database systems and repositories, as well as the introduction of new approaches such as machine learning. Written for the highly successful Methods in Molecular Biology series, the chapters include the kind of detailed implementation advice that leads to successful research results. 

1. Using GenBank and SRA

            Eric W. Sayers, Chris O’Sullivan, and Ilene Karsch-Mizrachi

 

2. Scripting Analyses of Genomes in Ensembl Plants

            Bruno Contreras-Moreira, Guy Naamati, Marc Rosello, James E. Allen, Sarah E. Hunt, Matthieu Muffato, Astrid Gall, and Paul Flicek

 

3. CyVerse for Reproducible Research: RNA-Seq Analysis

            Jason Williams

 

4. Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources

            Sven Redsun, Sam Hokin, Connor T. Cameron, Alan M. Cleary, Joel Berendzen, Sudhansu Dash, Anne V. Brown, Andrew Wilkey, Jacqueline D. Campbell, Wei Huang, Scott R. Kalberer, Nathan T. Weeks, Steven B. Cannon, and Andrew D. Farmer

 

5. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways

            Marcela Karey Tello-Ruiz, Pankaj Jaiswal, and Doreen Ware

 

6. CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource

            Mark Winfield, Paul Wilkinson, Amanda Burridge, Alexandra Allen, Jane Coghill, Christy Waterfall, Keith Edwards, and Gary Barker

 

7. The Barley and Wheat Pan-Genomes

            Nadia Kamal, Thomas Lux, Murukarthick Jayakodi, Georg Haberer, Heidrun Gundlach, Klaus F.X. Mayer, Martin Mascher, and Manuel Spannagl

 

8. Basics of Bash

            Robyn Anderson

 

9. Pipeline Automation via Snakemake

            Jakob Petereit

 

10. SciApps: An Automated Platform for Processing and Distribution of Plant Genomics Data

            Liya Wang, Zhenyuan Lu, Peter Van Buren, and Doreen Ware

 

11. Trimming and Validation of Illumina Short Reads Using Trimmomatic, Trinity Assembly, and Assessment of RNA-Seq Data

            Steven O. Sewe, Gonçalo Silva, Paulo Sicat, Susan E. Seal, and Paul Visendi

 

12. De Novo Assembly of Linked Reads Using Supernova 2.0

            Paul Visendi

 

13. Applications of Optical Mapping for Plant Genome Assembly and Structural Variation Detection

            Yuxuan Yuan

 

14. Making a Pangenome Using the Iterative Mapping Approach

            Cassandria Tay Fernandez

 

15. Construction of Practical Haplotype Graph (PHG) with the Whole Genome Sequence Data

            Pradeep Ruperao, Prasad Gandham, and Abhishek Rathore

 

16. Visualization Tools for Genomic Conservation

            Venkat Bandi, Carl Gutwin, Jorge Núñez Siri, Eric Neufeld, Andrew Sharpe, and Isobel Parkin

 

17. Annotation of Protein-Coding Genes in Plant Genomes

            Bhavna Hurgobin

 

18. Finding and Characterizing Repeats in Plant Genomes

            Jacques Nicolas, Sébastien Tempel, Anna-Sophie Fiston-Lavier, and Emira Cherif

 

19. Gene Co-Expression Network Analysis

            Juan D. Montenegro

 

20. Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies

            Philipp Emanuel Bayer

 

21. Managing High-Density Genotyping Data with Gigwa

            Guilhem Sempéré, Pierre Larmande, and Mathieu Rouard

 

22. Machine Learning for Image Analysis: Leaf Disease Segmentation

            Monica F. Danilevicz and Philipp E. Bayer

 

23. Analysis of Bisulphite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions

            HueyTyng Lee

 

24. Long Intergenic Non-Coding RNA (lincRNA) Discovery from Non-Strand Specific RNA-Seq Data

            Agnieszka Golicz

 

25. Linkage Disequilibrium Statistics and Block Visualization

            Jacob Marsh

 

26. Analysis of Small RNA Sequencing Data in Plants

            Vanika Garg and Rajeev K. Varshney

 

27. Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases

            Parul Gupta, Sushma Naithani, Justin Preece, Sunghwan Kim, Tiejun Cheng, Peter D'Eustachio, Justin Elser, Evan E. Bolton, and Pankaj Jaiswal

 

28. AgroLD: A Knowledge Graph Database for Plant Functional Genomics

            Pierre Larmande, Gildas Tagny Ngompe, Aravind Venkatesan, and Manuel Ruiz