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.
Access to full Lecture Notes





1.  Aug. 31 
Introduction Pairwise sequence alignment (lecture notes, pp. 1  9) PS0 due 10am on Tuesday, Sept. 7th 
Review biology and algorithms background  
2.  Sep. 2 
Global pairwise sequence alignment, class
notes pp. 19



3.  Sep. 7 
Local pairwise alignment Local alignment examples. PS0 DUE 10am 


4.  Sep. 9 
Introduction to Markov
chains (lecture notes pp.1719)
PS1 (due 11:59pm on Fri, Sep 17) Alignment template pdf, xlsx. solutions 7Eleven assignment 1 due midnight on Wed, Sept.22nd Alignment templates linear pdf, affine pdf, both xlsx. 


5.  Sep. 14 
Markov models chains (lecture notes pp.1729)


6.  Sep. 16 
Markov models of sequence evolution, JukesCantor model
PS1 due tomorrow (Friday) at 11:59pm PS2 out (due 11:59pm Mon, 9/28) solutions 


7.  Sep. 21 
Markov models of sequence evolution
Seven111 due tomorrow (Wednesday) at 5pm 

8.  Sep. 23 
Markov models of sequence evolution
PS3 out (due 11:59pm Sat, 10/02) solutions 

9.  Sep. 28 
Logodds scoring (lecture notes section 3.1)
PS2 due Monday at midnight 

10.  Sep. 30 
Amino acid substitution matrices (lecture notes,chapter 3)
PS4 out (due 11:59pm Fri, 10/08) solutions Enable Canvas course notifications to be notified when new assignments are posted. PS3 due on Saturday 

11.  Oct. 5 
Substitution matrices, cont'd


12.  Oct. 7 
PAM and BLOSUM,
PAM250,
BLOSUM62,
PAM30



13.  Oct. 12 
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 

14.  Oct. 14 
Mid semester break, NO CLASS. 

15.  Oct. 19 
BLOSUM matrices PS5 out (due 11:59pm Tues, 10/26) 

16.  Oct. 21 
Motifs, local multiple sequence alignment, PSSMs,
the Gibbs Sampler.



17.  Oct. 26 
The Gibbs sampler
7Eleven assignment 2 due 11:59pm, Tue, Nov 2nd. Enable Canvas course notifications to be notified when new assignments are posted. PS3 due on Saturday 

11.  Oct. 5 
Substitution matrices, cont'd


12.  Oct. 7 
PAM and BLOSUM,
PAM250,
BLOSUM62,
PAM30



13.  Oct. 12 
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 

14.  Oct. 14 
Mid semester break, NO CLASS. 

15.  Oct. 19 
BLOSUM matrices PS5 out (due 11:59pm Tues, 10/26). solutions 

16.  Oct. 21 
Motifs, local multiple sequence alignment, PSSMs,
the Gibbs Sampler.



17.  Oct. 26 
The Gibbs sampler
7Eleven assignment 2 due 11:59pm, Tue, Nov 2n PS5 DUE 11:59pm 


18.  Oct. 28 
Introduction to HMMs
PS6 out (due 11:59pm Friday 10/26) 
(electronic reserve). 

19.  Nov. 2 
HMMs: Recognition
7Eleven assignment 3 due 11:59pm, Tue, Nov 9th 

20.  Nov. 4 
HMMs recognition, cont'd
PS6 due tomorrow (Friday) at 11:59pm 


21.  Nov. 9 
HMMs: Modeling, parameter estimation



24.  Nov. 11 
HMMs: Modeling, parameter estimation
7Eleven assignment 4: pdf, latex, due 11:59pm, Fri, Nov 19th Yoon, 09 

23.  Nov. 16 
HMM topology, Profile
HMMs examples
PS7: due 11:59pm Wed. 11/24. pdf, latex 

24.  Nov. 18 
Multiple alignment using Profile HMMs
7Eleven4 is due tomorrow 


25.  Nov. 23 
BLAST statistics
PS7 is due tomorrow 

Protein multiple sequence alignment, Do and Katoh, 2008. (electronic reserves) 
Nov. 25 
Thanksgiving Holiday: No class
7Eleven assignment 5: pdf, due 11:59pm, Fri, Dec 3rd Altschul, 05 

26.  Nov. 30 
Blast statistics


27.  Dec. 2 
Blast statistics


Final exam 
Friday, Dec 10
5:308:30pm DH1211 
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. 
Last modified: August 31, 2021.