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.
Go to Google calendar (does not include links to homework or readings).





1.  Aug. 27 
PS0 due Tuesday, Sept. 3rd in class 
Review biology and algorithms background  
2.  Aug. 29 
Global pairwise sequence alignment,
pp 29



3.  Sep. 3 
Global and semiglobal alignment,
pp 611 PS0 DUE IN CLASS 


4.  Sep. 5 
Semiglobal and local pairwise alignment,
pp 1013 PS1 due 4pm Friday, Sept. 13th Additional alignment template 


5.  Sep. 10 
Introduction to Markov chains, pp
1520 Seven11 assignment 1 due Wednesday, Sept. 18th by 5pm Linear alignment template Affine gap alignment template 


6.  Sep. 12 
Markov models continued, pp 2027 PS1 due tomorrow (Friday) at 4pm PS2 due 4pm Friday, Sept. 20th 

7.  Sep. 17 
Markov models of DNA evolution,
pp 2732 Seven11 assignment 1 due tomorrow (Wednesday) at 5pm 


8.  Sep. 19 
Applications of Markov models of DNA evolution
pp 3238 PS2 due tomorrow (Friday) at 4pm PS3 due 4pm Friday, Sept. 27th 

9.  Sep. 24  More complex
applications of Markov models of DNA evolution
pp 3945 Seven11 assignment 2 due Wednesday, Oct. 2nd by 5pm 

10.  Sep. 26 
Logodds scoring
PS3 due tomorrow (Friday) at 4pm PS4 due 4pm Friday, Oct. 4th 

11.  Oct. 1  Amino acid
substitution, PAM matrices,
pp 5057 Seven11 assignment 2 due tomorrow (Wednesday) at 5pm 


12.  Oct. 3 
Amino acid subst. matrices cont'd pp 5860
PS4 due tomorrow (Friday) at 4pm Inclass EXAM I TUESDAY. 
Study guide  
13.  Oct. 8 
Inclass exam I This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Seven11 assignment 3 due Thursday, Oct. 17th by 5pm Page & Holmes, pp.187189. 
Study guide  
14.  Oct. 10  Comparing the PAM
and BLOSUM
matrices, pp
6166 Excel file of PAM and BLOSUM matrices PAM250, BLOSUM62 PAM30 PS5 due 4pm Monday, Oct. 21st 


15.  Oct. 15 
Modeling Motifs: PSSMs, pp 6770 Seven11 assignment 3 due Thursday at 5pm 


16.  Oct. 17 
The Gibbs Sampler, pp 7075 PS5 due MONDAY at 4pm 

17.  Oct. 22 
Hidden Markov Models, pp 7784 Seven11 assignment 4 due Wednesday, Oct. 30th by 5pm 


18.  Oct. 24 
HMMs continued, pp 7784
PS6 due 4pm Friday, Nov. 1st 

19.  Oct. 29 
Hidden Markov Models: Recognition, pp 8492
Seven11 assignment 4 due tomorrow (Wednesday) at 5pm 
(electronic reserve). 

20.  Oct. 31 
Hidden Markov Models: Recognition, pp 8492
PS6 due tomorrow (Friday) at 4pm 

21.  Nov. 5 
HMM design: Parameter estimation, topology, pp 92100
Inclass EXAM II THURSDAY. Study guide 


22.  Nov. 7 
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  
23.  Nov. 12 
Profile HMMs, Hidden Markov Models for global multiple alignment, pp 100108
Seven11 assignment 5 due Wednesday, Nov. 20th by 5pm 


24.  Nov. 14 
Blast heuristics, pp 115121
PS7 due 4pm Friday, Nov. 22nd 


25.  Nov. 19 
Gapped BLAST, pp 115121
Seven11 assignment 5 due tomorrow (Wednesday) at 5pm 

26.  Nov. 21 
BLAST statistics, pp 121132
PS7 due tomorrow (Friday) at 4pm PS8 Extra copies of the tables Excel version of the tables 


27.  Nov. 26  Class cancelled. Have a wonderful Thanksgiving holiday!  
Nov. 28 
Thanksgiving Holiday: No class 

28.  Dec. 3  Global multiple
sequence
alignment, pp
133138
Seven11 assignment 6 Altschul 05 


29.  Dec. 5 
Progressive multiple
alignment, pp
138142
PS8 due tomorrow (Friday) at 6pm Seven11 assignment 6 due Monday at 6pm PS9 due 4pm Wednesday, Dec. 11th This homework is optional. If you submit on time, I will drop your two lowest Problem Set grades. 

Protein multiple sequence alignment, Do and Katoh, 2008. (electronic reserves) 
Final exam  TBA 
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. 
The time and date of the final exam are determined by the
registrar's office and are beyond my control. You must take
the final exam at the time scheduled. Until the date of the final is determined, you should not make plans to leave for winter vacation before the end of the exam period. 
Last modified: September 12, 2019.
Maintained by Maureen Stolzer.