Computing for Bioinformatics Lectures for Fall 2007
Lecture 
Date 
Topics 
Overheads 
Handouts 

31 
Final Exam on Wednesday, December 12, from 12:50 PM in ITT 332 

30 
12/6 
Review for Final 


29 
12/4 



28 
11/29 
Section 7.4: Subquadratic LCS alignment 


27 
11/27 
Section 7.3: Block Alignment Problem using FourRussians speedup 


26 
11/15 
Section 7.2: SpaceEfficient Sequence Alignment 


25 
11/13 
Section 7.1: Merge Sort 


24 
11/8 
Chapter 7: Introduction to DivideandConquer Algorithms: Binary search; Master Theorem for solving recurrence equations 


23 
11/6 
Section 6.136.14: SimilarityBassed Approaches to Gene Prediction, and Spliced Alignment 
SimilarityBassed Approaches to Gene Prediction, and Spliced Alignment 

22 
11/1 
Section 6.12: Statistical Approaches to Gene Prediction 


21 
10/30 
Section 6.11: Gene Prediction: Regulation of Protein Production, and patterns of substitution within genes. 
Regulation of Protein Production and Patterns of Substituion within Genes 

20 
10/25 
Section 6.10: Multiple Sequence Alignment 


19 
10/23 
Sections 6.76.9: Local Alignment, Affine Gap Penalties 


18 
10/18 
Section 6.46.6: Edit Distance, Longest Common Subsequence, Global Alignment 


17 
10/16 
Section 6.3 Manhattan Tourist Problem 

16 
10/11 
Section 6.16.2: Dynamic Programming: Coinchange, Binomialcoefficient, memoization 


15 
10/9 
Return and Discuss Test 1 


14 
10/4 
Test 1 


13 
10/2 
Review for Test 1 


12 
9/27 
Section 5.3 – 5.4: Approximation Algorithms and ImprovedBreakpointReversalSort Analysis 

11 
9/25 
Section 5.153: Greedy Algorithms, Sorting by Reversals, Approximation Algorithms 


10 
9/20 
Section 4.84.9: Motif Finding Problem – BranchandBound 


9 
9/18 
Section 4.7: Motif Finding Problem, Search Trees 

8 
9/13 
Section 4.44.7: Regulatory Motifs in DNA, Profiles, Motif Finding Problem 

7 
9/11 
Sections 4.3 Backtracking Algorithms, Partial Digest Problem 


6 
9/6 
Sections 4.14.2 Brute Force Algorithms, Partial Digest Problem 


5 
9/4 
Sections 3.73.11: Protein Production, DNA sequencing, Genome Diversity 


4 
8/30 
Sections 3.13.6: Central Dogma of Molecular Biology 


3 
8/28 
Sections 2.102.11: BigOh, Tractable vs. Intractable Problems 

2 
8/23 
Sections 2.52.9: Recursion, More ProblemSolving Techniques 
More ProblemSolving Techniques (.ppt)


1 
8/21 
Chapter 1: Intro. To Bioinformatics Sections 2.12.4: Intro. To ProblemSolving Techniques 