Tentative Schedule for CPT S  471/571  Computational Genomics (Spring'18)

The course will be organized into four major parts: i) Approximate string matching, ii) Exact string matching, iii) Probabilistic modeling, and iv) Advanced applications.

Homework problems will be posted on a regular basis through the course of the semester. Due dates will be mentioned in the corresponding PDF that describes the problem question.

There will be  roughly 3-4 programming projects and multiple homework  problems which will be posted over the course of the semester. Due dates will be stated in the corresponding PDF/project webpages. 

The due dates mentioned below in this page are only a rough indicator and the actual due dates may vary. So please make sure you check the exact problem/project statement for the exact due dates.

All times mentioned are in US Pacific Time.

The following schedule is only tentative and is subject to change

Week Day Date Topic

Assignments*

Due Posting
1 Tu
1/9 Course Introduction, Computational biology & bioinformatics    

   
   
2
Tu
 1/16 Approximate matching, Global alignment , Local alignment, semi-global alignment    
 


   
3
Tu
 1/23 Affine gap penalty, Space-optimal alignments
   Programming Project 1


     
4
Tu 1/30 k-band algorithm, edit distance, LCS
 


 
 
5
Tu 2/6
Exact Matching, Lookup table, tries








6
Tu  2/13 Suffix Trees and Suffix arrays: definitions and applications
 


 


7
Tu 2/20
Suffix Tree and Suffix array construction algorithms




   

8
Tu  2/27 Lowest common ancestor problem








9
Tu  3/6 Instructor on travel - week (watch out for announcements prior to week)
571 students to finalize
survey project topics



   


10
Tu 3/13
SPRING BREAK WEEK - NO CLASS




   
 
11
Tu  3/20 More suffix tree applications
 




 
12
Tu  3/27 Probabilistic modeling, Markov chains, CpG islands
 


 
 
13
Tu 4/3
Hidden Markov Models: Algorithms and Applications
 


 


14
Tu  4/10 Genome graphs and assembly methods








15
Tu  4/17 Survey project presentations




   
 
16
Tu 4/24
Survey project presentations and course conclusion

 


 

 
 17     FINALS WEEK:

For All Students:
FINAL EXAM: Thursday, May 3, 08:00-10:00 in class

For CptS 571 students only:
Written report for survey project due on Thursday May 3, by midnight (23:59) through blackboard (hard deadline - no extension)

   
 

   

 



 


+ Denotes days when instructor will be on travel. Alternative arrangements for those classes will be communicated to the students as those days approach.