CS 482/682 Winter 2020

Time and Loc:

Tuesday and Thursday, 4:00-5:20pm. QNC-2501.


Bin Ma


Lecturer's Office hours: Monday 3-4pm. DC3345.


Korkmaz, Mustafa (mkorkmaz), Office hour: Friday 2:30-3:30pm, DC2310.

Course outline:

Please read a separate outline at the link above, especially for the assignment late policy, collaboration, and other ethical issues.

IMPORTANT NOTICE: Course format and evaluation change due to COVID-19

  1. The remaining 4 lectures from March 24 to April 2 will be delivered as recorded video. Links to the videos will be sent out as they become available.
  2. There will be no final exam. The marks you receive from midterm, assignments 1, 2, 3 and the upcoming assignment 4 will be re-weighted to calculate your final grade as follows:
  3. As we will not host in-person classes anymore, please fill in this term's teaching evaluation online at http://evaluate.uwaterloo.ca . You have until Friday April 3, 11:59 p.m. to complete the survey.

Important Dates:

  1. Assignment 1. Release Jan. 21. Due Jan. 31.
  2. Assignment 2. Release Jan. 30. Due Feb. 13.
  3. Reading week. Feb. 18-21.
  4. Midterm. Feb. 25. 4-5:30pm, MC 4063.
  5. Assignment 3. Release Feb. 27. Due Mar. 10.
  6. Assignment 4. Release Mar. 21. Due April 10, 11:59pm. Sample files: test.mgf, ups.fasta.
  7. Final exam. April 8. 9-11:30am. Final exam is cancelled.

Lecture notes:

Note: Efforts will be made to post notes before classes. But there is no guarantee, and there may be last minute changes to the notes before the class.
  1. Introduction
  2. Sequence Alignment
  3. Slightly Modified Models for Sequence Alignment
  4. Score and Significane
  5. Multiple Sequence Alignment
  6. Seeding Methods for Homology Search
  7. Phylogeny, chain-letter
  8. Suffix Tree and Array
  9. Hidden Markov Model and Gene Prediction
  10. Mass Spectrometry - Part 1. Introduction.
  11. Mass Spectrometry - Part 2. Database search for Peptide Identification
  12. sample mgf file , sample Mascot results.
  13. Course notes and video of the last 4 lectures will be made available on learn.uwaterloo.ca