Brubaker, Shane | Bioinformatics with Python Cookbook | E-Book | www.sack.de
E-Book

E-Book, Englisch, 618 Seiten

Brubaker, Shane Bioinformatics with Python Cookbook

Solve advanced computational biology problems and build production pipelines with Python and AI tools
4. Auflage 2025
ISBN: 978-1-83664-274-9
Verlag: De Gruyter
Format: EPUB
Kopierschutz: 0 - No protection

Solve advanced computational biology problems and build production pipelines with Python and AI tools

E-Book, Englisch, 618 Seiten

ISBN: 978-1-83664-274-9
Verlag: De Gruyter
Format: EPUB
Kopierschutz: 0 - No protection



If you've ever felt overwhelmed by the vast number of Python tools available for bioinformatics, you're not alone. The Bioinformatics with Python Cookbook is a recipe-based guide that explores practical approaches for solving classic bioinformatics challenges, showing you which Python packages work best for each task.
You'll start with the essential Python libraries for data science and bioinformatics, then move through key workflows in sequencing analysis, quality control, alignment, and variant calling. Along the way, you'll pick up modern coding practices, explore recent advances in bioinformatics research, and gain hands-on experience with libraries such as NumPy, pandas, and sci-kit learn. This book walks you through core bioinformatics tasks such as phylogenetic analysis and population genomics while familiarizing you with the wealth of modern public bioinformatics databases. You'll learn cloud computing approaches used by researchers, set up workflow orchestration systems for controlling bioinformatics pipelines, and see how AI and the use of large language models (LLMs) are reshaping the field-right down to designing proteins and DNA.
By the end of this book, you'll be ready to apply Python for real bioinformatics work and launch bioinformatics pipelines for your research.

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Weitere Infos & Material


Table of Contents


Preface


Free Benefits with Your Book


1


Computer Specifications and Python Setup


Technical requirements


Installing the required basic software with Anaconda


Getting ready


How to do it...


There’s more...


See Also


Installing the required software with Docker


Getting ready


How to do it...


See also


Introduction to Jupyter Notebook


How to do it…


See also


2


Basics of Data Manipulation


Using pandas to process vaccine-adverse events


Getting ready


How to do it...


There’s more...


See also


Dealing with the pitfalls of joining pandas DataFrames


Getting ready


How to do it...


There’s more...


Reducing the memory usage of pandas DataFrames


Getting ready


How to do it…


See also


3


Modern Coding Practices and AI-Generated Coding


Technical requirements


Using linting tools and style guides to write accurate, well-formed code


Getting ready


How to do it ...


There’s more …


See also…


Writing a simple bioinformatics file parser using AI


Getting ready


How to do it...


There’s more...


See also


Read alignment


How to do it...


See also


Writing tests with AI-assisted coding


How to do it...


There’s more...


See also


Code review with AI


How to do it...


There’s more...


See also


4


Data Science and Graphing


Technical requirements


Understanding NumPy as the engine behind Python data science and bioinformatics


Getting ready


How to do it…


See also


Introducing scikit-learn with PCA


Getting ready


How to do it...


There’s more...


See also


K-means clustering


Getting ready


How to do it...


There’s more...


See also


Exploring breast cancer traits using decision trees


Getting ready


How to do it...


See also


Learning more about Matplotlib for chart generation


Getting ready


How to do it...


There’s more...


Building a UMAP using Seaborn


Getting ready


How to do it...


There’s more ...


See also


5


Alignment and Variant Calling


Technical requirements


Quality control for sequencing data


Getting ready


How to do it...


There’s more...


See also


Tools for sequence manipulation


Getting ready


How to do it...


There’s more...


See also


Sequence alignment with BWA


Getting ready


How to do it...


There’s more...


See also


Variant calling with FreeBayes


Getting ready


How to do it...


There’s more...


See also


6


Annotation and Biological Interpretation


Technical requirements


Parsing and filtering variant files


Getting ready


How to do it...


There’s more...


See also


Annotating a prokaryotic genome


Getting ready


How to do it...


There’s more...


See also


Interpreting variants on gene structures


Getting ready


How to do it...


There’s more...


See also


Annotating proteins


Getting ready


How to do it...


There’s more...


See also


7


Genomes and Genome Assembly


Technical requirements


Accessing genome assemblies


Getting ready


How to do it...


There’s more...


See also


Working with graph genomes


Getting ready


How to do it...


There’s more...


See also


Long-read assembly with Raven


Getting ready


How to do it...


There’s more...


See also


Assessing genome quality with QUAST


Getting ready


How to do It...


There’s more...


See also


8


Accessing Public Databases


Technical requirements


Accessing GenBank and navigating NCBI databases


Getting ready


How to do it...


There’s more...


See also


Using the Sequence Read Archive


Getting ready


How to do it...


There’s more...


See also


Using PDB and UniProt


How to do it...


There’s more...


See also


9


Protein Structure and Proteomics


Technical requirements


Extracting information from PDB files


Getting ready


How to do it...


There’s more...


Computing molecular distances on a PDB file


Getting ready


How to do it...


There’s more...


Performing geometric operations


Getting ready


How to do it...


There’s more...


Animating proteins


Getting ready


How to do it...


There’s more...


See also


Performing proteomics analysis


Getting ready


How to do it...


There’s more...


See also


10


Phylogenetics


Technical requirements


Preparing a dataset for phylogenetic analysis


Getting ready


How to do it...


There’s more...


See also


Aligning genetic and genomic data


Getting ready


How to do it...


Comparing sequences


Getting ready


How to do it...


Reconstructing phylogenetic trees


Getting ready


How to do it...


There’s more...


See also


Playing recursively with trees


Getting ready


How to do it...


There’s more...


Visualizing phylogenetic data


Getting ready


How to do it...


There’s more...


11


Population Genetics


Technical requirements


Managing datasets with PLINK


Getting ready


How to do it...


There’s more...


See also


Using sgkit for population genetics analysis with xarray


Getting ready


How to do it...


There’s more...


Exploring a dataset with sgkit


Getting ready


How to do it...


There’s more...


See also


Analyzing population structure


Getting ready


How to do it...


See also


12


Metabolic Modeling and Other Applications


Technical requirements


Metabolic modeling with COBRApy


Getting ready


How to do it...


There’s more...


See also


Designing siRNAs with BioPython and ViennaRNA


Getting ready


How to do it...


There’s more...


See also


Predicting food properties using...




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