BioinformaticsAlgorithms

My solutions for the Coding Challenges in 'Bioinformatics Algorithms: An Active Learning Approach - 3rd Ed' by P. Compeau and P. Pevzner. All solutions were written in Python 3.10.4 using the Spyder 5.2.2 IDE.

Information about the book

This is the third edition of Bioinformatics Algorithms: an Active Learning Approach, one of the first textbooks to emerge from the revolution in online learning. A light hearted and analogy filled companion to the authors' acclaimed online courses, this book presents students with a dynamic approach to learning bioinformatics. It strikes a unique balance between practical challenges in modern biology and fundamental algorithmic ideas, thus capturing the interest of students of both biology and computer science. Each chapter begins with a biological question, such as "Are There Fragile Regions in the Human Genome?" or "Which DNA Patterns Play the Role of Molecular Clocks?" and then steadily develops the algorithmic sophistication required to answer this question. Hundreds of exercises are incorporated directly into the text as soon as they are needed; readers can test their knowledge through automated coding challenges on Rosalind, a popular platform for learning bioinformatics through programming.

- Book description on Amazon.com

A link to the book can be found here. An interactive version can be read (partly for free) here.

Table of contents

1. Where in the Genome Does Replication Begin? - Algorithmic Warmup
2. Which DNA Patterns Play the Role of Molecular Clocks? - Randomized Algorithms
3. How Do We Assemble Genomes? - Graph Algorithms
4. How Do We Sequence Antibiotics? - Brute Force Algoritms
5. How Do We Compare Biological Sequences? - Dynamic Programming
6. Are There Fragile Regions in the Human Genome? - Combinatorial Algorithms
7. Which Animal Gave Us SARS? - Evolutionary Tree Reconstruction
8. How Did Yeast Become a Wine-Maker? - Clustering Algorithms
9. How Do We Locate Disease-Causing Mutations? - Combinatorial Pattern Matching
10. Why Have Biologists Still Not Developed an HIV Vaccine? - Hidden Markov Models
11. Was T. rex Just a Big Chicken? - Computational Proteomics