We will now perform an example of simulating selection with simuPOP. We will perform a simple case with dominant mutation on a single loci and also a complex case with two loci using epistatic effects. The epistatic effect will have a mutation on an SNP. This is required to confer advantage and another mutation on another SNP that adds up to the previous one (but does nothing on its own); this was inspired by the very real case of malaria resistance to the sulfadoxine/pyrimethamine drug, which always requires a mutation on the DHFR gene, which can be enhanced with a mutation on the DHPS gene; if you are interested in knowing more, refer to the Origin and Evolution of Sulfadoxine Resistant Plasmodium falciparum article from Vinayak et al on PLoS Pathogens at http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1000830.
Bioinformatics with Python Cookbook
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Bioinformatics with Python Cookbook
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Overview of this book
Table of Contents (16 chapters)
Bioinformatics with Python Cookbook
Credits
About the Author
About the Reviewers
www.PacktPub.com
Preface
Free Chapter
Python and the Surrounding Software Ecology
Next-generation Sequencing
Working with Genomes
Population Genetics
Population Genetics Simulation
Phylogenetics
Using the Protein Data Bank
Other Topics in Bioinformatics
Python for Big Genomics Datasets
Index
Customer Reviews