CSE 5095:  String Algorithms and Application in Bioinformatics, Spring 2013,  Instructor: Yufeng Wu
Tentative Class Schedule (subject to change)

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

2
Lecture 2. Karp-Rabin. Aho-Corasick. Other related algorithms. HW1
3
Lecture 3. Suffix tree. Constant-time 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 four-Russians 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 high-throughput 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.