CS 482/682 Winter 2018
Time and Loc:
Tuesday and Thursday, 1:00-2:20am. RCH 109.
Lecturer's Office hours: Wednesday 4-5pm. DC3345.
Jian Li, jian.li, Office hour: Friday 2-3, DC 2102.
Please read a separate outline at the link above, especially for the
assignment late policy, collaboration, and other ethical issues.
- Jan. 4. First lecture.
11 15: assignment 1 release
- Jan. 25: assignment 2 release
- Jan. 31: assignment 1 due before midnight
- Feb. 11: assignment 2 due before midnight.
- Feb. 15: in class midterm. Here is a sample midterm from several years ago.
- Feb. 19-23. University's study days (no lectures or office hours).
- Mar. 1: assignment 3 release
- Mar. 15: assignment 3 due before midnight.
- Mar. 13: assignment 4 release.
test.mgf, ups.fasta, a4-test.peaksdb.csv.
- Mar. 30: assignment 4 due before midnight.
- April 3. Last Lecture.
- TBD. Final exam.
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
- Suffix Tree and Array
- Seeding Methods for Homology Search
- Genome Sequencing
- NGS readings and resources
- A Brief Introduction to Mass Spectrometry
- Database search for Peptide Identification with MS
- Peptide De Novo Sequencing
- Peptide and Protein De Novo Sequencing
- Hidden Markov Model
- Phylogeny, chain-letter.pdf