Algorithms in Bioinformatics course

(March - April 2019)

This repository contains presentations and code for Algorithms in Bioinformatics course

Overview

1. Algorithm definition, algorithms complexity, Big O notation
2. Python basics
3. String algorithms: string match, substring search, edit distance, alignment
4. Divide and Conquer algorithms. Dynamic programming.
5. Suffix array, Burrows Wheeler Transform
6. Fuzzy search, heuristic algorithms
7. Graphs, basic graph algorithms: DFS, BFS, topological sort
8. Genome assembly algorithms, De Bruijn graphs
9. Computational Mass Spectrometry algorithms
10. Phylogeny Tree Algorithms

Lectures

№	Lecture	Links	Homework
1	What is algorithm? How do we compare algorithms? Algorithms complexity	--	--
2	Python Basics, String Algorithms	lecture2 lecture 3	--
3	Alignment Algorithms	lecture4	ba9m BWT Matching ba5f Local Alignment
4	Graph Algorithms, Assembly Algorithms	lecture5	ba3h De Bruijn Assembly ba3j Paired De Bruijn Assembly
5	Hidden Markov Models	lecture6	ba10g HMM Alignment
6	Phylogeny Tree Algorithms	lecture7	ba7d UPGMA ba7e Neighbor Joining
7	Mass Spectrometry Algorithms	lecture8	ba11e Sequence a Peptide