Introduction to Bioinformatics Algorithms
Summer 2011
, Xi'an Jiaotong University

Instructor: Yufeng Wu

Lecture: Tuesday and Thursday 7:30-9:30 pm.

Office Hour: By appointment.

Anouncements.


Course Description
. See the Syllabus.



Schedule.

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: Burrows-Wheeler transform.
Wikipedia's entry for Burrows-Wheeler 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.