CS 482/682 Winter 2017
Time and Loc:
Monday and Wednesday, 10:00-11:20am. QNC 1506.
Lecturer's Office hours: Tuesday 10:00am-12:00pm. DC3345. Starting from Jan. 24.
Jia Rong Wu, jr2wu, Office hour: Friday 1-2pm, DC 2102. Jia will mark the first 2 assignments.
Mustafa Korkmax, mkorkmaz, Office hour: Thursday 3-4pm, DC3580. Mustafa will mark the last 2 assignments.
Please read a separate outline at the link above, especially for the
assignment late policy, collaboration, and other ethical issues.
We will make course related announcements on Piazza site. Please register to receive the announcements.
You can also post questions and discussions on the site, as well as answering questions for other studnets.
- Jan. 4. First lecture.
- Jan. 9: assignment 1 release
- Jan. 22: assignment 1 due
- Jan. 23: assignment 2 release
- Feb. 5: assignment 2 due (receive 0.5 bonus mark if submit before this due date).
- Feb. 12: assignment 2 extended due date (no bonus mark).
- Feb. 13: assignment 3 release
- Feb. 15: in class midterm. Here is a sample midterm from several years ago.
- Feb. 20-24. University's study days (no lectures or office hours).
- Mar. 12: assignment 3 due
- Mar. 13: assignment 4 release. Data files:
test.mgf, ups.fasta, a4-test.peaksdb.csv.
- Mar. 26: assignment 4 due
- April 3. Last Lecture.
- April 17: Final exam. 7:30-10:00pm, MC4058.
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.
The items with no links are copied from an earlier offering of this course, and are subject to changes.
- Sequence Alignment
- Slightly Modified Models for Sequence Alignment
- Score and Significane
- Multiple Sequence Alignment
- Suffix Tree and Array
- Seeding Methods for Homology Search
- Genome Sequencing
- A Brief Introduction to Mass Spectrometry
- Database search for Peptide Identification with MS
- Peptide De Novo Sequencing;
Also a webpage for a mass table.
- Hidden Markov Model
- Phylogeny; chain-letter.pdf
- Review; A list of important concepts.