The materials in the "Assigned Reading" column are directly
related to the topics covered in class. Readings under
"Additional Topics" are strictly optional and will not be covered
on the exams.
In some cases, the same material is covered in
more than one textbook. You have the choice of selecting the text
that presents a treatment of the material most to your liking. It
is your responsibility to make sure that you understand the
material covered in class and you may read as many or as few of
these texts needed to achieve that goal.





1.  Aug. 30 
Introduction to computational biology and genomics
part 1
, part 2
PS0 due September 6th.  Review biology and algorithms background  
2.  Sep. 1 
Global pairwise sequence alignment
PAIRWISE ALIGNMENT NOTES Alignment example  distance scoring. 


3.  Sep. 6 
Global and semiglobal alignment
Alignment example  similarity scoring. PS0 DUE 


4.  Sep. 8 
Semiglobal and local pairwise alignment local alignment examples 
courtesy Dr. M. Singh, Princeton University 

5.  Sep. 13 
Local sequence alignment local alignment examples Global multiple sequence alignment GLOBAL MSA NOTES 

Protein multiple sequence alignment , Do and Katoh, 2008. 
6.  Sep. 15 
The progressive multiple alignment heuristic
PS1 due Friday, Sept 23rd 

7.  Sep. 20 
Introduction to Markov chains
MARKOV CHAIN NOTES 


8.  Sep. 22 
Markov chains, continued. PS1 due tomorrow (9/23) at 4pm Lit assignment 1: Due Sep 29 

9.  Sep. 27 
Markov models of sequence evolution,
JukesCantor model SEQUENCE EVOLUTION MODEL NOTES 
Durbin, et al: 8.2, pp. 193  197 only (electronic reserves)  
10.  Sep. 29 
Markov models of DNA sequence evolution, cont'd. Lit1 due at 4pm PS2 due Oct 7th 

11.  Oct. 4 
Markov models of amino acid replacement
PAM MATRIX LECTURE NOTES 


12.  Oct. 6 
Markov models of amino acid replacement BLOSUM MATRIX LECTURE NOTES PS2 due tomorrow (Oct 7th) at 4pm 


13.  Oct. 11 
Amino acid substitution matrices, continued.
Comparing PAM and Blosum matrices. PAM30, BLOSUM62, PAM250, BLOSUM45 

14.  Oct. 13 
Inclass exam I This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Study guide 

15.  Oct. 18 
Database searching
BLAST HEURISTIC NOTES Midterm scores 


16.  Oct. 20 
Blast heuristic continued.
PS3 due Friday, Oct 28 
Gapped BLAST
: a new generation of protein database
search programs. Altschul et al., Nucl. Acids Res. (1997)
25 (17). Assigned reading: pp. 33893394 only. 

17.  Oct. 25 
BLAST STATISTICS LECTURE NOTES

 
18.  Oct. 27 
Blast statistics and information content, continued.
PS3 due tomorrow. PS4 due Friday, Nov 4 Lit assignment 2: Due Nov 3rd, 4pm. 

19.  Nov. 1 
Local multiple alignment, PSSM's, the Gibbs sampler PSSM/GIBBS SAMPLER NOTES PSSM example, with and without pseudocounts 


20.  Nov. 3 
The Gibbs Sampler 

21.  Nov. 8 
The Gibbs Sampler 

22.  Nov. 10 
Inclass exam II This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Study guide Exam II scores 

23.  Nov. 15 
Hidden Markov Models HMM LECTURE NOTES  Part 1 PS5 due Tuesday, Nov 22 
Hidden Markov Models in Computational
Biology: Applications to Protein
Modeling, Krogh et al., JMB 235, pp 15011531,(1994). (electronic reserve). 

24.  Nov. 17 
HMMs cont'd.
The Forward and Viterbi algorithms Forward example 

25.  Nov. 22 
No class.
PS5 due at 4pm Lit assignment 3: due Nov 29th 

Nov. 24 
Thanksgiving Holiday: No class


26.  Nov. 29 
Hidden Markov Models: Decoding Viterbi example PS6 due Monday, Dec 5 

27.  Dec. 1 
HMMs: Modeling, parameter estimation HMM LECTURE NOTES  Part 2 

28.  Dec. 6 
Profile HMM's.
Optional PS7 due Monday, Dec 5 due Tuesday, 13th at 1pm if you are submitting PS 7 for credit. 


29.  Dec. 8  Profile HMMs 


Review  Dec 14, 12:00  2:00 
Porter Hall A19A
Question/Answer session. Bring your questions with you. 

Final Exam  Dec 15, 5:30pm  8:30pm 
Final exam
This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. 
Study guide The exam covers the entire semester, but with a strong emphasis on the last third of the course. 