CSE 5840:  String Algorithms and Application in Bioinformatics, Fall 2015,  Instructor: Yufeng Wu
Tentative Class Schedule (subject to change)

Week
Lectures
Assignments
1
Algorithms for exact string matching
Inroduction to string matching. Z algorithm. KMP. And other classic string matching algorithms.
HW1
2
Suffix tree. Constant-time LCA.
3
Suffix array. Applications of suffix trees and suffix arrays.
4
Approximate string matching. HW2
5
Multiple sequence alignment: latest development.

6
BWT.
HW3
7
Applications and properties of string processing
Applications in high-throughput sequencing: reads mapping; genome assembly.

8
Applications in high-throughput sequencing: k-mer counting; structural variation finding.
9
Applications in high-throughput sequencing: ancient DNA analysis; whole genome comparison.
10
Algorithms on text coding and compression
11
Compression of sequence data.

12
Applications in high-throughput sequencing: e.g. functional genomics, RNA-seq, etc.

13
Student presentations
Student
paper presentation.

14
Student paper presentation and project presentation.
Project report due.