CS 482/682 Winter 2020
Time and Loc:
Tuesday and Thursday, 4:00-5:20pm. QNC-2501.
Lecturer's Office hours: Monday 3-4pm. DC3345.
Korkmaz, Mustafa (mkorkmaz), Office hour: Friday 2:30-3:30pm, DC2310.
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
- 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.
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:
- First 3 assignments, 42% (14+14+14).
- Assignment 4, 28%
- Midterm exam, 30%
- Final exam, Cancelled
- 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.
- Assignment 1. Release Jan. 21. Due Jan. 31.
- Assignment 2. Release Jan. 30. Due Feb. 13.
- Reading week. Feb. 18-21.
- Midterm. Feb. 25. 4-5:30pm, MC 4063.
- Assignment 3. Release Feb. 27. Due Mar. 10.
- Assignment 4. Release Mar. 21. Due April 10, 11:59pm.
Sample files: test.mgf, ups.fasta.
Final exam. April 8. 9-11:30am. Final exam is cancelled.
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.
- Sequence Alignment
- Slightly Modified Models for Sequence Alignment
- Score and Significane
- Multiple Sequence Alignment
- Seeding Methods for Homology Search
- Phylogeny, chain-letter
- Suffix Tree and Array
- Hidden Markov Model and Gene Prediction
- Mass Spectrometry - Part 1. Introduction.
- Mass Spectrometry - Part 2. Database search for Peptide Identification
sample mgf file ,
sample Mascot results.
- Course notes and video of the last 4 lectures will be made available on learn.uwaterloo.ca