Tentative Schedule for CPT S 571/471 Computational Genomics (Spring'17)

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 3 programming projects 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

Class Day Date Topic

Assignments*

Due Posting
1 M 1/9 Course Introduction, Computational biology & bioinformatics    
2  W  
   
3   F   Approximate matching, Global alignment    
  M 1/16 MLK Day - All University Holiday    
4   W   Global alignment, Local alignment    
5   F        
6 M 1/23 Affine gap penalty, Semi-global alignment   Program 1
7   W   space-optimal alignment & Hirschberg technique    
8   F


Problem set 1
9 M 1/30 k-band algorithm

10   W   Edit distance, Longest common subsequence problem    Homework 1
11   F   Exact Matching, Lookup tables, tries
 
12 M 2/6 PATRICIA tree, tries: definitions    Problem set 2
13 W        
14   F   Suffix trees: definition & application Program 1 due   
  M 2/13
   
15 W        
16 F    Suffix links
 
17 M 2/20 President's Day - Class Holiday    
18 W    Instructor on travel    
19   F   Suffix tree construction: McCreight algorithm  
20 M 2/27  Instructor on travel    
21   W+    Instructor on travel    
22   F   Suffix arrays + LCP    Program 2
23 M 3/6 Lowest common ancestor problem (Bender-Farach algo)  
24   W        
25   F  

 
  M 3/13 SPRING BREAK    
    W      
    F      
26 M 3/20 More suffix tree applications Finalize survey project  
27   W   Probabilistic modeling, Markov models, CpG islands    
28   F        
29 M

   Survey Project
30   W  

 
31   F   Hidden Markov models (HMM), Viterbi algorithm  Program 2 due
 
32 M 4/3 Forward and backward algorithm   Program 3
33   W   PA3 discussion    
34   F   Homework problems discussion    
35 M 4/10 PA2 demos    
36   W   PA2 demos    
37   F   PA2 demos    
38 M 4/17 no class (work on PA3 and survey presentations)
 
39   W   Survey project presentations :

   
40   F   Survey project presentations :

   
41 M 4/24 Survey project presentations  :

   
42   W  
Program 3  
43   F  
   
     5/1 FINALS WEEK:

All students:

1) FINAL EXAM: Wednesday, May 3, 3:10-5:10pm in class (for all students)

2) For 571 students: Written report for survey project due on Thrusday, May 4, by NOON through OSBLE+ (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.