Plant bioinformatics : methods and protocols
著者
書誌事項
Plant bioinformatics : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2443）（Springer protocols）
Humana Press, c2022
3rd ed
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注記
Previous ed.: 2016
Includes bibliographical references and index
内容説明・目次
内容説明
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.
目次
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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