Week 
Lectures 
Assignments 
1 
Algorithms for exact string matching Lecture 1. Inroduction to string matching. Z algorithm. KMP. BoyerMoore. 

2 
Lecture 2. KarpRabin. AhoCorasick. Other related algorithms.  HW1 
3 
Lecture 3.
Suffix tree. Constanttime LCA. 

4 
Lecture 4. Suffix array. Applications of suffix trees and suffix arrays.  HW2 
5 
Extensions to basic string matching Lecture 5. Sequences with dynamic programming. The fourRussians trick. Approximate string matching. 

6 
Lecture 6:
More Approximate string matching. Blast,
hashing and seeding. 
HW3 
7 
Lecture 7: Probabilistic models of strings and patterns.  
8 
Lecture 8: BWT. 

9 
Applications and properties of string
processing Lecture 9: algorithms on text coding and compression 

10 
Lecture 10: applications in highthroughput sequencing.  HW4 
11 
No class (due to travel)  
12 
Lecture 11: more recent topics on string algorithms.  
13 
Student presentations Student paper presentation 1. 

14 
Student paper
presentation 2. 

15 
Final exam 
Project report due. 