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R Bioinformatics Cookbook - Second Edition

You're reading from  R Bioinformatics Cookbook - Second Edition

Product type Book
Published in Oct 2023
Publisher Packt
ISBN-13 9781837634279
Pages 396 pages
Edition 2nd Edition
Languages
Author (1):
Dan MacLean Dan MacLean
Profile icon Dan MacLean
Toc

Table of Contents (16) Chapters close

Preface 1. Chapter 1: Setting Up Your R Bioinformatics Working Environment 2. Chapter 2: Loading, Tidying, and Cleaning Data in the tidyverse 3. Chapter 3: ggplot2 and Extensions for Publication Quality Plots 4. Chapter 4: Using Quarto to Make Data-Rich Reports, Presentations, and Websites 5. Chapter 5: Easily Performing Statistical Tests Using Linear Models 6. Chapter 6: Performing Quantitative RNA-seq 7. Chapter 7: Finding Genetic Variants with HTS Data 8. Chapter 8: Searching Gene and Protein Sequences for Domains and Motifs 9. Chapter 9: Phylogenetic Analysis and Visualization 10. Chapter 10: Analyzing Gene Annotations 11. Chapter 11: Machine Learning with mlr3 12. Chapter 12: Functional Programming with purrr and base R 13. Chapter 13: Turbo-Charging Development in R with ChatGPT 14. Index 15. Other Books You May Enjoy

Finding orthologue candidates using reciprocal BLASTs

In genomics, orthology refers to the relationship between genes from different species that evolved from a common ancestral gene through speciation. Orthologous genes typically have the same function and structure and play similar roles in different organisms, even if they have diverged over time.

Orthology has many important uses in bioinformatics. Orthology can be used to infer the function of a gene in a newly sequenced genome based on its similarity to known genes in other species. This can be especially useful for identifying genes that are involved in specific biological processes or pathways. Orthologous genes can be used to compare the genomes of different organisms and study the evolution of gene families. By identifying which genes are conserved across different species, researchers can gain insights into the evolutionary history of those genes and the organisms that carry them.

Orthology can be inferred using various...

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