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Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook

By : Tiago Antao
3.5 (4)
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Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook

3.5 (4)
By: Tiago Antao

Overview of this book

Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data. This book covers next-generation sequencing, genomics, metagenomics, population genetics, phylogenetics, and proteomics. You'll learn modern programming techniques to analyze large amounts of biological data. With the help of real-world examples, you'll convert, analyze, and visualize datasets using various Python tools and libraries. This book will help you get a better understanding of working with a Galaxy server, which is the most widely used bioinformatics web-based pipeline system. This updated edition also includes advanced next-generation sequencing filtering techniques. You'll also explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks such as Dask and Spark. By the end of this book, you'll be able to use and implement modern programming techniques and frameworks to deal with the ever-increasing deluge of bioinformatics data.
Table of Contents (12 chapters)
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Simulating selection

We will now perform an example of simulating selection with simuPOP. We will perform a simple case with dominant mutation on a single locus, along with a complex case with two loci using epistatic effects. The epistatic effect will have a required mutation on a main SNP. While this mutation is required to confer advantage, another mutation on another SNP adds up to the previous one (but does nothing on its own); this was inspired by the very real case of malarial resistance to the Sulfadoxine/Pyrimethamine drug, which always requires a mutation on the Dihydrofolate Reductase (DHFR) gene, which can be enhanced with a mutation on the Deoxyhypusine Synthase (DHPS) gene. If you are interested in finding out more, refer to the Origin and Evolution of Sulfadoxine Resistant Plasmodium falciparum article from Vinayak et al. on PLOS Pathogens at http://journals.plos...

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