03511/03711 - Syllabus

Computational Molecular Biology and Genomics - Syllabus, Fall 2025

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. 26 Introduction
Pairwise sequence alignment ( lecture notes , pp. 1 - 3)

Review biology and algorithms background
2. Aug. 28
Readyness Quiz


3. Sep. 2
Global pairwise sequence alignment
( lecture notes , Section 1.1)

Global alignment examples
similarity scoring.
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. 4 Local pairwise alignment
    ( lecture notes , Section 1.2)

    Local alignment examples.
    Local pairwise alignment
    - Setubal and Meidanis, p. 55 ,
    - Durbin, 23-24
    5. Sep. 9 Global multiple sequence alignment



    Global multiple alignment using dynamic programming
    - Setubal and Meidanis, 69-72 (electronic reserve)
    - Durbin, 6.1 -- 6.3
    6. Sep. 11
    7. Sep. 16
    8. Sep. 18
    9. Sep. 23
    10. Sep. 25
    11. Sep. 30
    12. Oct. 2
    13. Oct. 7
    14. Oct. 9
    Oct. 14 & Oct. 16
    Mid semester break, NO CLASS.
    15. Oct. 21
    16. Oct. 23
    17. Oct. 28
    18. Oct. 30
    Nov. 4
    Election Day; No class

    19. Nov. 6
    20. Nov. 11
    21. Nov. 13
    22. Nov. 18
    23. Nov. 20
    24. Nov. 25
    Nov. 27
    Thanksgiving Holiday: No class

    25. Dec. 2
    26. Dec. 4
    Final exam
    TBD
    Final exam
    The exam covers the entire semester, but with a strong emphasis on the last third of the course.
    This exam is closed book. You may bring four pages (or two pages, front and back) of your own notes. You will not need a calculator.
    		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.


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    Last modified: Aug. 25 2025.