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

    ( lecture notes , Sections 2.1, 2.2)

    Global multiple alignment using dynamic programming
    - Setubal and Meidanis, pp. 69-72, 79-80.
    - Durbin, 6.1 -- 6.3
    6. Sep. 11 Global multiple alignment: heuristic methods
    Today's slides

    Lecture notes , Sections 2.3

    Global multiple alignment: heuristic methods
    - Durbin, 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.
    7. Sep. 16 Introduction to Markov chains. Lecture Notes Sections 3.1


    Markov Chain background
    - Ewens and Grant, 4.4-4.8
    - Durbin et al. , 48-51 (Section 3.1)
    8. Sep. 18 Markov chains, Lecture Notes Sections 3.1

    Problem set 2, due Fri, 9/26, at 11:59pm.
    9. Sep. 23 Markov models of sequence evolution
    Lecture Notes Section 3.2

    Today's slides
    Periodicity handout

    Models of nucleotide substitution
    - Durbin et al. , 8.2, pp. 193 - 197 only
    10. Sep. 25 Applications of DNA substitution models

    Lecture Notes Section 3.3
    Today's slides

    Problem set 2, due tomorrow at midnight.
    11. Sep. 30
    Applications of DNA substitution models:
    Correcting for multiple substitutions.   Lecture Notes Section 3.3.3
    Log odds scoring   Lecture Notes Section 4.1

    Today's slides

     EXAM 1:
       7:30pm - 9:30pm, DH 5403
    - 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 9.

    12. Oct. 2
    Phylogenetics

    13. Oct. 7
    Amino acid substitution matrices
    Log odds scoring   Lecture Notes Section 4.1

    Today's slides


    14. Oct. 9
    Amino acid substitution matrices
    PAM matrices Lecture Notes Section 4.2

    PAM30 , PAM250

    Problem Set 3, due Friday October 24th.
    pdf,
    latex zip file
    Substitution matrices:
    - Setubal and Meidanis, 80-84;
    - Mount, pp. 76-89;
    - Durbin et al, pp. 14-16
    Oct. 14 & Oct. 16
    Mid semester break, NO CLASS.
    15. Oct. 21
    Amino acid substitution matrices
    PAM matrices (review) Lecture Notes Section 4.2
    BLOSUM matrices Lecture Notes Section 4.3


    BLOSUM62
    Today's slides
    /
    BLOSUM Matrices:
    - Ewens and Grant, 6.5.2.
    - Amino acid substitution matrices from protein blocks, Henikoff S, Henikoff JG., PNAS 89(22):10915-9, 1992
    16. Oct. 23
    Searching sequence databases
    The Basic Local Alignment Search Tool (Blast). Lecture notes, section 5.1

    Mid-semester scores

    Problem set 3, due tomorrow at midnight.
    Blast 1990
    - Setubal and Meidanis, 84-87
    - Basic local alignment search tool, Altschul et al. , J. Mol. Bio., 1990
    = Gapped BLAST Altschul et al. , Nucl. Acids Res.., 1997
    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.