Date 
Topic 
Reading 
Assignment  FAQs 
Jan.4 
Introduction to biological and linguistic strings/sequences; formal representation; overview of main problems 
Gusfield Ch.10 Durbin Ch.1 
 
Jan.6 
Introduction to string edit distance, dynamic programming and approximate alignment; motivation for efficient exact match 
Gusfield Ch.11 Durbin Ch.2 
 
Jan.11 
Deterministic exact string matching (a): simple approaches; intro to KnuthMorrisPratt and BoyerMoore algorithms 
Gusfield Ch.1 
 
Jan.13 
Deterministic exact string matching (b): KnuthMorrisPratt and BoyerMoore algorithms 
Gusfield Ch.2 
HW1  faq1 
Jan.18 
Deterministic exact string matching (c): AhoCorasick algorithm for sets of patterns; regular expression patterns 
Gusfield Ch.3 
 
Jan.20 
No class 

 
Jan.25 
Suffix trees: introduction and lineartime construction algorithms; some applications (exact string matching); suffix automata and suffix arrays 
Gusfield Ch.56 
 
Jan.27 
Student presentations on HW1 variations 

HW2  
Feb.1 
Efficient approximate matching: linear space, bounded approximate matching and exclusion methods. Brief introduction to HMM alignment models 
Gusfield Ch.12 Durbin Ch.3 
 
Feb.3 
Hidden Markov models for tagging, bracketing, segmentation and pairwise alignment; dynamic programming; finitestate transducers 
Durbin Ch.4 
 
Feb.8 
HMM parameter reestimation; forwardbackward for Expectation Maximization; Learning HMM alignment models; pronunciation alignments 
Ristad and Yianilos (1998) 
 
Feb.10 
In class midterm 

HW 3  
Feb.15 
Discriminative Modeling for Gene Prediction 
Bernal et al. (2007) 
 
Feb.17 
Introduction to multiple sequence alignments; families; profile HMMs; Perceptron Algorithm for profiles 
Durbin Ch.5 
 
Feb.22 
Aligning multiple sequences; Minimum sumofpairs alignment; higher dimensional dynamic programming; iterative pairwise alignment 
Durbin Ch.6 Gusfield Ch.14 
 
Feb.24 
Introduction to phylogenic tree building; Ultrametric and additive distance trees; distancebased tree construction; parsimony 
Durbin Ch.7 Gusfield Ch.17 
HW 4 Final proj  
Mar.1 
Probabilistic models of phylogeny 
Durbin Ch.8 
 
Mar.3 
Context free modeling for Protein and RNA secondary structure; Context free inference; RNA structure prediction 
Durbin Ch.9 Searls (2002) 
 
Mar.8 
RNA structure prediction (cont.); Protein folding; Mildly contextsensitive models 
Durbin Ch.10 Hockenmaier et al. (2006) 
 
Mar.10 
Guest lecture (Chris Whelan) on topics in sequencing 

 
Mar.15 
In class final presentations 

 
Mar.17 
In class final presentations 

 