CS 482/682 Winter 2022

Time and Loc:

Tuesday and Thursday, 11:30AM - 12:50PM. The lectures will be online initially. When we return to classroom teaching later this term, it will be in MC4042.

You should have received an email containing the zoom link for joining the online lectures. If not, send the instructor an email to request for that link.

Lecturer:

Bin Ma

Email:

Lecturer's virtual office hours: Wednesday 11am-12pm zoom online. The same link for the online lectures will be used for the online office hour.

TA:

Guo, Runsheng (r9guo), Office hour: Mon.&Fri. 9-10am. Zoom link has been sent to your mailbox. If you cannot find it, email TA for the link.

Course outline:

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

Important Dates:

  1. Jan. 6. First lecture.
  2. Feb. 21-25. Reading week.
  3. April 5. Last lecture.
  4. April 19, 4-6:30pm, Final exam. MC4063

Assignments

  1. Assn1: Implement a sequence alignment program and use it to determine SARS-Cov2 variants. Released Jan. 20. Due Feb. 6.

    Update 2022.01.24: To make things simpler, we will use a simplified FASTA format for the input files, where each entry in the file takes exactly two lines: the first starts with a ‘>’ sign and is the “header line” or “annotation line”. The second is the actual sequence.

  2. Assn2: Write a program to distinguish natural and random peptide sequences. Released Feb. 3. Due Feb. 18
  3. Assn3: Write a program to identify peptides from mass spectrometry data. Supplied files:

    Release Feb. 17. Due Mar. 13.

  4. Assn4: Use existing software to predict and study the structure of SARS-Cov2 spike protein. Released Mar. 17. Due April. 3.

Piazza

We will use Piazza for course-related discussion. The course link at Piazza is https://piazza.com/class/ky3gj562oaq4wp.

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; Hand-written notes: ( 2022-01-11 lecture) ( 2022-01-13 lecture) ( 2022-01-18 lecture)
  3. Slightly Modified Models for Sequence Alignment ( 2022-01-18 lecture) ( 2022-01-20 lecture)
  4. Score and Significane ( 2022-01-25 lecture) ( 2022-01-27 lecture)
  5. Multiple Sequence Alignment ( 2022-01-27 lecture) ( 2022-02-01 lecture)
  6. Seeding Methods for Homology Search ( 2022-02-03 lecture) ( 2022-02-08 lecture) ( 2022-02-10 lecture)
  7. Proteomics and Mass Spectrometry - Part 1. Introduction. ( 2022-02-10 lecture) ( 2022-02-15 lecture)
  8. Proteomics and Mass Spectrometry - Part 1. Database Search. ( 2022-02-15 lecture) ( 2022-02-17, 2022-03-01 lectures)
  9. Proteomics and Mass Spectrometry - Database Search Details. ( 2022-03-01 lecture)
  10. Proteomics and Mass Spectrometry - De Novo Sequencing. ( 2022-03-03 lecture)
  11. Quantification and an Application in Cancer Detection. ( 2022-03-08 lecture)
  12. Spectrum Prediction with Deep Learning. ( 2022-03-08 lecture) ( 2022-03-10 lecture)
  13. Protein Structure Prediction with Deep Learning. ( 2022-03-15 lecture)
  14. Hidden Markov Model and Gene Prediction ( 2022-03-17 lecture) ( 2022-03-22 lecture)
  15. Phylogeny; An article about the evolution of chain letters. ( 2022-03-22 lecture) ( 2022-03-24 lecture) ( 2022-03-29 lecture)
  16. Suffix Tree and Suffix Array; ( 2022-03-31 lecture) ( 2022-04-05 lecture)
  17. Review; (No handwriting notes.)