Week 
Topics 
References 
Assignments 
4 
6/9: Final exam and review. 6/7: Genome assembly from short sequencing reads. 
There are many pointers to
genome assembly, for example: a short intro. to genome assembly 

3 
6/2: Pairwise
sequence
alignment algorithms and linear space sequence
alignment. 5/31: Hidden Markov models. Lecture to be given by J. Wang. 
There are many course notes on
sequence alignments. For example, course notes from U. of Toronto A tutorial on hidden Markov models by Rabiner This is a widely used tutorial on HMM. 

2 
5/26: Hidden
markov
models. Lecture to be given by J.
Wang. 5/24: BurrowsWheeler transform. 
Wikipedia's
entry for BurrowsWheeler transform A paper on pattern matching with BWT 
HW1 Due: 5/31 in class. Programming assignment Due: 6/9 in class. 
1 
5/19 Suffix
tree and suffix
array algorithms. 5/17: Exact string matching in bioinformatics. Suffix tree and its applications. 
A survey of
suffix tree and suffix array by S. Aluru An introduction to suffix tree This covers many topics taught in the class. 