CS 482/682 Winter 2017

Time and Loc:

Monday and Wednesday, 10:00-11:20am. QNC 1506.


Bin Ma


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.

Course outline:

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

Piazza site:

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.

Important dates:

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. The items with no links are copied from an earlier offering of this course, and are subject to changes.
  1. Introduction
  2. Sequence Alignment
  3. Slightly Modified Models for Sequence Alignment
  4. Score and Significane
  5. Multiple Sequence Alignment
  6. Suffix Tree and Array
  7. Seeding Methods for Homology Search
  8. Genome Sequencing
  9. A Brief Introduction to Mass Spectrometry
  10. Database search for Peptide Identification with MS
  11. Peptide De Novo Sequencing; Also a webpage for a mass table.
  12. Hidden Markov Model
  13. Phylogeny; chain-letter.pdf
  14. Review; A list of important concepts.
  15. Review

Other Material