CS 482/682 Winter 2018

Time and Loc:

Tuesday and Thursday, 1:00-2:20am. RCH 109.


Bin Ma


Lecturer's Office hours: Wednesday 4-5pm. DC3345.


Jian Li, jian.li, Office hour: Friday 2-3, DC 2102.

Course outline:

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

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.
  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. NGS readings and resources
  10. A Brief Introduction to Mass Spectrometry
  11. Database search for Peptide Identification with MS
  12. Peptide De Novo Sequencing
  13. Peptide and Protein De Novo Sequencing
  14. Quantification
  15. Hidden Markov Model
  16. Phylogeny, chain-letter.pdf
  17. Review