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Bioinformatics with Python Cookbook

You're reading from Bioinformatics with Python Cookbook Solve advanced computational biology problems and build production pipelines with Python and AI tools

Product type Paperback

Published in Dec 2025

Publisher Packt

ISBN-13 9781836642756

Length 618 pages

Edition 4th Edition

Languages

Python

Tools

Jupyter

Concepts

Data Science

Author (1):

Shane Brubaker

View More author details

Table of Contents (22) Chapters

Preface

1. Chapter 1: Computer Specifications and Python Setup

2. Chapter 2: Basics of Data Manipulation FREE CHAPTER

3. Chapter 3: Modern Coding Practices and AI-Generated Coding

4. Chapter 4: Data Science and Graphing

5. Chapter 5: Alignment and Variant Calling

6. Chapter 6: Annotation and Biological Interpretation

7. Chapter 7: Genomes and Genome Assembly

8. Chapter 8: Accessing Public Databases

9. Chapter 9: Protein Structure and Proteomics

10. Chapter 10: Phylogenetics

11. Chapter 11: Population Genetics

12. Chapter 12: Metabolic Modeling and Other Applications

13. Chapter 13: Genome Editing

14. Chapter 14: Cloud Basics

15. Chapter 15: Workflow Systems

16. Chapter 16: More Workflow Systems

17. Chapter 17: Deep Learning and LLMs for Nucleic Acid and Protein Design

18. Chapter 18: Single-Cell Technology and Imaging

19. Chapter 19: Unlock Your Exclusive Benefits

Unlock this Book’s Free Benefits in 3 Easy Steps

20. Index

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21. Other Books You May Enjoy

Technical requirements

For this chapter, we will be using the following tools and packages:

Pyfastx
NetworkX
Matplotlib
Raven
QUAST

You will be instructed on how to install each package as we go. You can find the code for this chapter at https://github.com/PacktPublishing/Bioinformatics-with-Python-Cookbook-Fourth-Edition/tree/main/Ch07.

The rest of the chapter is locked

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Tech Concepts

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Authors (1)

Shane Brubaker

Shane Brubaker

Shane Brubaker is a bioinformatics manager living in California. He believes in the power of bioinformatics as an interdisciplinary science to save lives and transform society. Shane has applied bioinformatics in areas ranging from synthetic biology to human health. Over the years, he has taught courses in computer science and biology, co-founded BayBifx, a leading Bay Area bioinformatics networking event, and mentored many bioinformatics professionals. Shane is passionate about training and providing opportunities for the next generation of scientists.

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