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. 29 
Introduction Pairwise sequence alignment (lecture notes, pp. 1  13) 
Review biology and algorithms background  
2.  Aug. 31 
Global pairwise sequence alignment, class
notes pp. 19



3.  Sep. 5 
Local pairwise alignment Local alignment examples. Expected alignment scores 


4.  Sep. 7 
Introdution to Markov chains, class
notes Sections 2.1, 2.2.1  2.2.3



5.  Sep. 12 
Markov models of sequence evolution (lecture notes, Section 2.3) Today's slides 


6.  Sep. 14 
Markov models of sequence evolution,
applications of DNA substitution models (lecture notes,
Sections 2.3 and 2.4)


7.  Sep. 19 
Markov models of sequence evolution,
applications of DNA substitution models (lecture notes,
Sections 2.4)
Today's slides 

8.  Sep. 21 
Logodds scoring 

9.  Sep. 26 
Amino acid substitution matrices: PAM matrices
(lecture notes, Section 3.2)



10.  Sep. 28 
Amino acid substitution matrices: PAM matrices
(lecture notes, Section 3.2) PAM250, PAM30 

11.  Oct. 3 
Substitution matrices, continued. BLOSUM62 


12.  Oct. 5 
Motifs, local multiple sequence alignment, PSSMs


13.  Oct. 10 
Inclass
EXAM  This exam is closed book. You may bring two pages (or one page, front and back) of your own notes.  The exam covers material covered in Lectures 1 through 7. Study Guide 

14.  Oct. 12 
Motifs, local multiple sequence alignment, PSSMs PSSM class notes: Section 4.1 Today's slides 


Oct. 17 & Oct. 19 
Mid semester break, NO CLASS. 

15.  Oct. 24 
Gibbs Sampler 


16.  Oct. 26 
Gibbs Sampler continued 

17.  Oct. 31 
Hidden Markov Models Lecture Notes, Chapter 5 

18.  Nov. 2 
Designing HMMs: topology and parameter estimation with
labeled sequences Today's slides 


Nov. 7 
Election Day; No class


19.

Nov. 9 
HMMs: Recognition algorithms
Today's
slides



20.  Nov. 14 
HMMs: the Backward Algorithm, posterior decoding, BaumWelch



21.  Nov. 16 
Profile
HMMs


Tutorial on Hidden Markov Models, L.R. Rabiner, Proc. IEEE, 1989 
22.  Nov. 21 
Profile HMMs; Multiple alignment using Profile HMMs. Lecture notes,
section 5.7


Nov. 23 
Thanksgiving Holiday: No class


23.  Nov. 28 
Searching sequence databases The Basic Local Alignment Search Tool (Blast). 


24.  Nov. 30 
Blast Statistics Today's slides 


25.  Dec. 5 
The statistics of database searching Today's slides 

26.  Dec. 7 
Blast statistics
continued,
Today's
slides



Dec 14 1pm 4pm WEH 7500 
Study Guide 
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: Dec 07, 2023.