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.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, Semiglobal alignment  Program
1 

7  W  spaceoptimal alignment & Hirschberg technique  
8  F  Problem set 1 

9  M  1/30  kband 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 (BenderFarach 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,
3:105:10pm 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.