Plant Bioinformatics : Methods and Protocols / edited by David Edwards.

Format:

Book

Contributor:

Edwards, David, Editor.

SpringerLink (Online service)

Series:

Springer Protocols (Springer-12345)

Methods in molecular biology 1940-6029 ; 2443

Methods in Molecular Biology, 1940-6029 ; 2443

Language:

English

Subjects (All):

Bioinformatics.

Botany.

Plant Science.

Local Subjects:

Bioinformatics.

Plant Science.

Physical Description:

1 online resource (XIV, 544 pages) : 116 illustrations, 108 illustrations in color.

Edition:

3rd ed. 2022.

Contained In:

Springer Nature eBook

Place of Publication:

New York, NY : Springer US : Imprint: Humana, 2022.

System Details:

text file PDF

Summary:

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.

Contents:

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 Bisulphite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions

Long Intergenic Non-Coding 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.

Other Format:

Printed edition:

ISBN:

978-1-0716-2067-0

9781071620670

Access Restriction:

Restricted for use by site license.