Harnessing Genomic Tools for Crop Improvement: A Software User Manual for Transforming Geneticists to Genomicists is an essential resource aimed at users of crop improvement software. This manual offers comprehensive guidance to understand and utilize molecular data derived from genetics and breeding experiments. By presenting step-by-step instructions for various genomics-related software, such as genetic diversity (DARWIN) and QTL mapping (QTL Cartographer), it serves both novice and expert users. The book simplifies the complicated processes of genome-wide association mapping, haplotype analysis, and marker-assisted breeding, ensuring accurate interpretation and application of the results.
In addition to the step-by-step guides, the book explores cutting-edge bioinformatics tools such as databases, BLAST, primer designing, and sequence alignment. Definitions and terminology clarifications are provided, along with detailed interpretations of the software outputs through case studies. This comprehensive manual is invaluable to scientists, students, and post-doctoral fellows interested in plant and animal genetics, making it a vital asset in the field of genomics.
1. Basic bioinformatics software
2. Molecular marker development
3. ARMS-PCR, CAPS, dCAPS, etc 3. NGS analysis
4. Genetic diversity and population structure analysis
5. QTL mapping
6. Genome-wide association mapping
7. Statistical models for Genomic selection
8. Haplotype analysis
9. Analysis of Gene regulatory networks
10. Transcriptome analysis
11. MiRNA structure and target prediction tools
12. Designing of guide RNA for CRISPR gene editing
13. Protein Interaction Network Analysis: Essential Tools and Resources
14. Navigating in silico drug discovery: A hands-on guide with Auto Dock Vina, ChemDraw and Chimera for structure simulation
15. Machine learning techniques for gene prediction
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