Edwards David (ed.) Plant Bioinformatics: Methods and Protocols

3rd edition. — Humana Press, 2022. — 1173 p. — (Methods in Molecular Biology 2443). — ISBN 978-1-0716-2067-0.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.Using GenBank and SRA
Scripting Analyses of Genomes in Ensembl Plants
CyVerse for Reproducible Research:​ RNA-Seq Analysis
Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources
Gramene:​ A Resource for Comparative Analysis of Plants Genomes and Pathways
CerealsDB:​ A Whistle-Stop Tour of an Open Access SNP Resource
The Barley and Wheat Pan-Genomes
Basics of Bash
Pipeline Automation via Snakemake
SciApps:​ An Automated Platform for Processing and Distribution of Plant Genomics Data
Trimming and Validation of Illumina Short Reads Using Trimmomatic, Trinity Assembly, and Assessment of RNA-Seq Data
De Novo Assembly of Linked Reads Using Supernova 2.​0
Applications of Optical Mapping for Plant Genome Assembly and Structural Variation Detection
Making a Pangenome Using the Iterative Mapping Approach
Construction of Practical Haplotype Graph (PHG) with the Whole-Genome Sequence Data
Visualization Tools for Genomic Conservation
Annotation of Protein-Coding Genes in Plant Genomes
Finding and Characterizing Repeats in Plant Genomes
Gene Co-expression Network Analysis
Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies
Managing High-Density Genotyping Data with Gigwa
Machine Learning for Image Analysis:​ Leaf Disease Segmentation
Analysis of Bisulfite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions
Long Intergenic Noncoding RNA (lincRNA) Discovery from Non-Strand-Specific RNA-Seq Data
Linkage Disequilibrium Statistics and Block Visualization
Analysis of Small RNA Sequencing Data in Plants
Plant Reactome and PubChem:​ The Plant Pathway and (Bio)Chemical Entity Knowledgebases
AgroLD:​ A Knowledge Graph Database for Plant Functional Genomics