CiNii 図書 - 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. Authoritative and up-to-date, Plant Bioinformatics: Methods and Protocols, Third Edition will aid researchers exploring the broad comparison of species that will drive future plant research, crop breeding, and bioinformatics developments that allow us to understand and manipulate the heritable differences between individuals and populations. Chapters 2, 3, and 26 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

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, Goncalo 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 Nunez 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, Sebastien 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 Sempere, 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

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Plant bioinformatics : methods and protocols

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