Week Date Topic Slides / notes Reading Assignment
1 8/23 Introduction Slides What is Bioinfo, Jones&Pevzner Chap3, MBWB Chap1.A, Chap3.A, 3.B, 3.E  
2 8/28 Introduction to molecular biology Slides | notes  
8/30 Global sequence alignment Slides

What is Dynamic Programming, J&P Ch 6.1-6.6, 7.2, Durbin Ch 2 linear-space alg review,

 
3 9/4 Linear-space alignment, bounded alignment Slides HW1 out
9/6 Affine gap alignment, Local sequence alignment Slides J&P Ch 6.7-6.9, Durbin 2.3 BLOSUM62  
4 9/11 Alignment Statistics Slides

J&P 6.6-6.8, Durbin 2.5-2.6,

  
9/13 BLAST Slides BLAST  
5 9/18 Multiple sequence alignment Slides J&P 6.10, Durbin 6.1-6.4 HW1 due
9/20 Intro to Prob and Stat Slides Intro to Prob and Stat HW1 solutions
6 9/25 Hidden Markov models

Slides 1 Slides 2

Durbin Ch 3, J&P Ch 11, Tutorial on hmm and applications on speech recognition  
9/27  
7 10/2 Hidden Markov model Slides
Slides 		Durbin Ch 4, 5, J&P 6.11-6.14; GeneScan HW2 out
10/4  
8 10/9 Hidden Markov model applications
String algorithms and applications		 Slides Slides Pattern Matching in Strings Project 1
10/11 HW2 due
9 10/16 String algorithms and applications Slides
Slides 		   
10/18  
10 10/23 Motif finding Slides
Slides 		What are DNA motifs?
How to find motifs?
Gibbs Sampler
Practical strategies		 HW2 Out
10/25  
11 10/30 TBD   How do RNA folding algorithms work?  
11/1 Motif finding Slides
Slides 		Choose topic for final project
12 11/6

RNA secondary structure prediction

Slides    
11/8 HW2 due solution
13 11/13 Introduction to microarray Slides    
11/15  
14 11/20 Microarray data analysis Slides    
11/22 No class (thanksgiving)    
15 11/27

Phylogeny

     HW3 out
11/29  
16 12/4 No class      
12/6

HW3 due

Final project report due
17 12/11 Final presentation