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Bioinformatics with Python Cookbook - Fourth Edition

Name: Bioinformatics with Python Cookbook - Fourth Edition
Author: Shane Brubaker
ISBN: 9781836642756

by Shane Brubaker

December 2025

Beginner to intermediate

618 pages

14h 48m

English

Packt Publishing

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Bioinformatics with Python Cookbook
About the author
About the reviewers
Preface
Who this book is forWhat this book coversTo get the most out of this bookDownload the example code filesConventions usedSectionsGetting readyHow to do it…How it works…There’s more…See alsoGet in touchShare your thoughtsFree Benefits with Your BookHow to Unlock
Chapter 1: Computer Specifications and Python Setup
Technical requirementsInstalling the required basic software with AnacondaGetting readyHow to do it...There’s more...See AlsoInstalling the required software with DockerGetting readyHow to do it...See alsoIntroduction to Jupyter NotebookHow to do it…See also
Chapter 2: Basics of Data Manipulation
Using pandas to process vaccine-adverse eventsGetting readyHow to do it...There’s more...See alsoDealing with the pitfalls of joining pandas DataFramesGetting readyHow to do it...There’s more...Reducing the memory usage of pandas DataFramesGetting readyHow to do it…See also
Chapter 3: Modern Coding Practices and AI-Generated Coding
Technical requirementsUsing linting tools and style guides to write accurate, well-formed codeGetting readyHow to do it ...There’s more …See also…Writing a simple bioinformatics file parser using AIGetting readyHow to do it...There’s more...See alsoRead alignmentHow to do it...See alsoWriting tests with AI-assisted codingHow to do it...There’s more...See alsoCode review with AIHow to do it...There’s more...See also
Chapter 4: Data Science and Graphing
Technical requirementsUnderstanding NumPy as the engine behind Python data science and bioinformaticsGetting readyHow to do it…See alsoIntroducing scikit-learn with PCAGetting readyHow to do it...There’s more...See alsoK-means clusteringGetting readyHow to do it...There’s more...See alsoExploring breast cancer traits using decision treesGetting readyHow to do it...See alsoLearning more about Matplotlib for chart generationGetting readyHow to do it...There’s more...Building a UMAP using SeabornGetting readyHow to do it...There’s more ...See also
Chapter 5: Alignment and Variant Calling
Technical requirementsQuality control for sequencing dataGetting readyHow to do it...There’s more...See alsoTools for sequence manipulationGetting readyHow to do it...There’s more...See alsoSequence alignment with BWAGetting readyHow to do it...There’s more...See alsoVariant calling with FreeBayesGetting readyHow to do it...There’s more...See also
Chapter 6: Annotation and Biological Interpretation
Technical requirementsParsing and filtering variant filesGetting readyHow to do it...There’s more...See alsoAnnotating a prokaryotic genomeGetting readyHow to do it...There’s more...See alsoInterpreting variants on gene structuresGetting readyHow to do it...There’s more...See alsoAnnotating proteinsGetting readyHow to do it...There’s more...See also

Chapter 7: Genomes and Genome Assembly
Technical requirementsAccessing genome assembliesGetting readyHow to do it...There’s more...See alsoWorking with graph genomesGetting readyHow to do it...There’s more...See alsoLong-read assembly with RavenGetting readyHow to do it...There’s more...See alsoAssessing genome quality with QUASTGetting readyHow to do It...There’s more...See also
Chapter 8: Accessing Public Databases
Technical requirementsAccessing GenBank and navigating NCBI databasesGetting readyHow to do it...There’s more...See alsoUsing the Sequence Read ArchiveGetting readyHow to do it...There’s more...See alsoUsing PDB and UniProtHow to do it...There’s more...See also
Chapter 9: Protein Structure and Proteomics
Technical requirementsExtracting information from PDB filesGetting readyHow to do it...There’s more...Computing molecular distances on a PDB fileGetting readyHow to do it...There’s more...Performing geometric operationsGetting readyHow to do it...There’s more...Animating proteinsGetting readyHow to do it...There’s more...See alsoPerforming proteomics analysisGetting readyHow to do it...There’s more...See also
Chapter 10: Phylogenetics
Technical requirementsPreparing a dataset for phylogenetic analysisGetting readyHow to do it...There’s more...See alsoAligning genetic and genomic dataGetting readyHow to do it...Comparing sequencesGetting readyHow to do it...Reconstructing phylogenetic treesGetting readyHow to do it...There’s more...See alsoPlaying recursively with treesGetting readyHow to do it...There’s more...Visualizing phylogenetic dataGetting readyHow to do it...There’s more...
Chapter 11: Population Genetics
Technical requirementsManaging datasets with PLINKGetting readyHow to do it...There’s more...See alsoUsing sgkit for population genetics analysis with xarrayGetting readyHow to do it...There’s more...Exploring a dataset with sgkitGetting readyHow to do it...There’s more...See alsoAnalyzing population structureGetting readyHow to do it...See also
Chapter 12: Metabolic Modeling and Other Applications
Technical requirementsMetabolic modeling with COBRApyGetting readyHow to do it...There’s more...See alsoDesigning siRNAs with BioPython and ViennaRNAGetting readyHow to do it...There’s more...See alsoPredicting food properties using bioinformaticsGetting readyHow to do it...There’s more...Discovering genes to make novel moleculesGetting readyHow to do it...There’s more...See also
Chapter 13: Genome Editing
Technical requirementsDesigning guide RNAs for genome editingGetting readyHow to do it...There’s more...See alsoCounting barcodes in a genomic libraryGetting readyHow to do it...There’s more...See alsoUsing nanopore data to resolve genome editsGetting readyHow to do it...There’s more...See also
Chapter 14: Cloud Basics
Technical requirementsSetting up an AWS accountGetting readyHow to do it...There’s more...See alsoBuilding cloud components using boto3Getting readyHow to do it...There’s more...See alsoBuilding a container in AWS ECRGetting readyHow to do it...There’s more...See also
Chapter 15: Workflow Systems
Technical requirementsIntroducing GalaxyGetting readyHow to do it...There’s more...Writing a bioinformatics workflow with SnakemakeGetting readyHow to do it...There’s more...See alsoWriting a bioinformatics workflow with NextflowGetting readyHow to do it...There’s more...See also
Chapter 16: More Workflow Systems
Technical requirementsBuilding a bioinformatics workflow with FlyteGetting readyHow to do it...There’s more...See alsoLaunching a bioinformatics orchestrator with AWS Step FunctionsGetting readyHow to do it...There’s more...See also
Chapter 17: Deep Learning and LLMs for Nucleic Acid and Protein Design
Technical requirementsMachine learning with PyTorchGetting readyHow to do it...There’s more...See alsoDesigning proteins with LLMsGetting readyHow to do it...There’s more...See alsoDesigning DNA with LLMsGetting readyHow to do it...There’s more...See also
Chapter 18: Single-Cell Technology and Imaging
Technical requirementsBuilding microfluidics devicesGetting readyHow to do it...There’s more...See alsoAnalyzing single-cell dataGetting readyHow to do it...There’s more...See alsoStudying biological image dataGetting readyHow to do it...There’s more...See alsoMapping the brainGetting readyHow to do it...There’s more...See alsoGlossary
Chapter 19: Unlock Your Exclusive Benefits
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Content preview from Bioinformatics with Python Cookbook - Fourth Edition

5 Alignment and Variant Calling

In this chapter, we will cover some of the core aspects of bioinformatics work. We will deeply explore how to examine the quality of sequencing data for different technologies. We will also go deeper into various tools for manipulating relevant file formats and briefly cover some recent advances in data compression for bioinformatics files. Then, we’ll discuss how sequencing data is aligned to reference sequences and review the importance of different aspects of sequencing algorithms. Finally, we’ll get into variant calling and see how the information resulting from an alignment can be used to find critical biological insights about people and organisms.

In this chapter, we’re going to cover the following main ...

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Bioinformatics with Python Cookbook - Third Edition

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ISBN: 9781836642756

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Bioinformatics with Python Cookbook - Fourth Edition

by Shane Brubaker

5

Alignment and Variant Calling

Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
and much more.