03511/03711 - Syllabus

Computational Molecular Biology and Genomics - Syllabus, Fall 2026

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 Lecture Notes


  
CLASS
DATE
TOPICS
ASSIGNED READING
ADDITIONAL TOPICS
1. Aug. 25 Introduction
Pairwise sequence alignment
(lecture notes, pp. 1 - 3)

Review biology and algorithms background
2. Aug. 27
Readiness Quiz


Solutions
3. Sep. 1 Global pairwise sequence alignment
( lecture notes , Section 1.1)

Global alignment examples
Alighment example used in class.
Practise problems, similarity scoring.
Practise problems, distance scoring.
Global pairwise alignment
- Setubal and Meidanis, 47-57 , 89-92 , 96-98 ;
- Durbin, 17-24

  • Saving space,
    - Setubal and Meidanis, 58-60; (physical reserve)
  • General and affine gap penalty functions,
    - Setubal and Meidanis, 60-66 (physical reserve)
    - Durbin, 29-30
  • Semi-global alignment
    - Setubal and Meidanis, 56-57 ,
    • 4. Sep. 3 Local pairwise alignment
    ( lecture notes , Section 1.2)

    Local alignment examples.
    Local pairwise alignment
    - Setubal and Meidanis, p. 55 ,
    - Durbin, 23-24
    5. Sep. 8 Global multiple sequence alignment

       Lecture notes, Chapter 2.
    Today's slides
    Global multiple alignment
    - Setubal and Meidanis, pp. 69-72, 79-80.
    - Durbin, 6.1 -- 6.4
    		 Protein multiple sequence alignment, Do and Katoh, 2008.

    A survey on the algorithm and development of multiple sequence alignment, Zhang et al, 2022.

    6. Sep. 10 Evolutionary trees (I)

    Today's slides
    Page and Holmes Molecular Evolution : A Phylogenetic Approach.
    Tree properties: Sections 2.1.1 - 2.1.4.
    Inferring Molecular phylogeny: Section 6.1.
    Maximum Parsimony: Section 6.4.
    		 
    7. Sep. 15 Evolutionary trees, continued.

    Today's slides
    Markov Chain background
    - Ewens and Grant, 4.4-4.8
    - Durbin et al. , 48-51 (Section 3.1)
    8. Sep. 17 Introduction to Markov chains.
    Lecture Notes Sections 3.1


    9. Sep. 22
    Markov chains
    Periodicity, Lecture notes 3.1.4
    Limiting and stationary distributions, Lecture notes 3.1.5

    Markov models of sequence evolution
    Lecture Notes 3.2


    Models of nucleotide substitution
    - Durbin et al. , 8.2, pp. 193 - 197 only
    10. Sep. 24
    11. Sep. 29
    Sep. 30 EXAM 1   7:30pm - 9:30pm
    12. Oct. 1
    13. Oct. 6
    14. Oct. 8
    Oct. 13 & Oct. 15
    15. Oct. 20
    16. Oct. 22
    17. Oct. 27
    18. Oct. 29
    Nov. 3
    19. Nov. 5
    20. Nov. 10
    21. Nov. 12
    Nov. 12 EXAM 2:   7:30pm - 9:30pm
    22. Nov. 17
    23. Nov. 19
    24. Nov. 24
    Nov. 26
    25. Dec. 1
    26. Dec. 3
    Final exam
    TBD


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    Last modified: Aug. 23, 2026.