03511 - Syllabus

Computational Molecular Biology and Genomics - Syllabus, Fall 2021


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


   
CLASS
DATE
TOPICS
ASSIGNED READING
ADDITIONAL TOPICS
1.   Aug. 31 Introduction
Pairwise sequence alignment (lecture notes, pp. 1 - 9)

PS0 due 10am on Tuesday, Sept. 7th
Review biology and algorithms background
2.  Sep. 2 Global pairwise sequence alignment, class notes pp. 1-9

Alignment examples
distance scoring.
similarity 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,
  • 3.  Sep. 7 Local pairwise alignment
          Local alignment examples.

    PS0 DUE 10am  
    Local pairwise alignment
    - Setubal and Meidanis, p. 55,
    - Durbin, 23-24
    4.  Sep. 9 Introduction to Markov chains (lecture notes pp.17-19)

    PS1 (due 11:59pm on Fri, Sep 17)
        Alignment template pdf, xlsx.
       solutions

    7Eleven assignment 1 due midnight on Wed, Sept.22nd
        Alignment templates linear pdf, affine pdf, both xlsx.
    Markov Chain background
    - Ewens and Grant, 4.4-4.8
    - Durbin et al., 48-51 (Section 3.1)
    5.  Sep. 14 Markov models chains (lecture notes pp.17-29)

     
    6.  Sep. 16 Markov models of sequence evolution, Jukes-Cantor model

    PS1 due tomorrow (Friday) at 11:59pm

    PS2 out (due 11:59pm Mon, 9/28)    solutions
    Models of nucleotide substitution
    - Durbin et al., 8.2, pp. 193 - 197 only
     
    7.  Sep. 21 Markov models of sequence evolution

    Seven11-1 due tomorrow (Wednesday) at 5pm
     
    8.  Sep. 23 Markov models of sequence evolution


    PS3 out (due 11:59pm Sat, 10/02)    solutions
     
    9.  Sep. 28 Log-odds scoring (lecture notes section 3.1)

    PS2 due Monday at midnight
     
    10.  Sep. 30 Amino acid substitution matrices (lecture notes,chapter 3)

    PS4 out (due 11:59pm Fri, 10/08)    solutions
       Enable Canvas course notifications to be notified when new assignments are posted.
    PS3 due on Saturday


    Substitution matrices:
    - Setubal and Meidanis, 80-84;
    - Mount, pp. 76-89;
    - Durbin et al, pp. 14-16
     
    11.  Oct. 5 Substitution matrices, cont'd

    12.  Oct. 7 PAM and BLOSUM,   PAM250,   BLOSUM62,   PAM30

    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 (electronic reserve)
     
    13.  Oct. 12 In-class EXAM I
    This exam is closed book. You may bring two pages (or one page, front and back) of your own notes.

    Study guide
       
    14.  Oct. 14

    Mid semester break, NO CLASS.


    15.  Oct. 19 BLOSUM matrices


        PS5 out (due 11:59pm Tues, 10/26)
       
    16.  Oct. 21 Motifs, local multiple sequence alignment, PSSMs, the Gibbs Sampler.
    slides,

    PSSM example, with and without pseudocounts.
    Gibbs sampler
    Ewens and Grant, 211-215. (electronic reserve).
    Theoretical framework, convergence proofs
    - Ewens and Grant, 10.5.2, (physical reserves).
    - Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment, Lawrence et al., Science. 1993 262(5131):208-14.
    - Explaining the Gibbs sampler, G. Casella & E. I. George, The American Statistician, 46:167-174, 1992
    17.  Oct. 26 The Gibbs sampler

    7Eleven assignment 2 due 11:59pm, Tue, Nov 2nd.    Enable Canvas course notifications to be notified when new assignments are posted.
    PS3 due on Saturday


    Substitution matrices:
    - Setubal and Meidanis, 80-84;
    - Mount, pp. 76-89;
    - Durbin et al, pp. 14-16
     
    11.  Oct. 5 Substitution matrices, cont'd

    12.  Oct. 7 PAM and BLOSUM,   PAM250,   BLOSUM62,   PAM30

    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 (electronic reserve)
     
    13.  Oct. 12 In-class EXAM I
    This exam is closed book. You may bring two pages (or one page, front and back) of your own notes.

    Study guide
       
    14.  Oct. 14

    Mid semester break, NO CLASS.


    15.  Oct. 19 BLOSUM matrices


        PS5 out (due 11:59pm Tues, 10/26).    solutions

       
    16.  Oct. 21 Motifs, local multiple sequence alignment, PSSMs, the Gibbs Sampler.
    slides,

    PSSM example, with and without pseudocounts.
    Gibbs sampler
    Ewens and Grant, 211-215. (electronic reserve).
    Theoretical framework, convergence proofs
    - Ewens and Grant, 10.5.2, (physical reserves).
    - Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment, Lawrence et al., Science. 1993 262(5131):208-14.
    - Explaining the Gibbs sampler, G. Casella & E. I. George, The American Statistician, 46:167-174, 1992
    17.  Oct. 26 The Gibbs sampler

    7Eleven assignment 2 due 11:59pm, Tue, Nov 2n

        PS5 DUE 11:59pm  
    What is an HMM?
    - Ewens & Grant, 327-329
    - Durbin et al, 53-55
    18.  Oct. 28 Introduction to HMMs

        PS6 out (due 11:59pm Friday 10/26)


    Viterbi, Forward, Backward algorithms
    - Durbin et al, 55 - 61
    - Ewens and Grant, 329-332
    (electronic reserve).
     
    19.  Nov. 2 HMMs: Recognition
    Viterbi example,
    Forward example.


    7Eleven assignment 3 due 11:59pm, Tue, Nov 9th


     
    20.  Nov. 4 HMMs recognition, cont'd

    PS6 due tomorrow (Friday) at 11:59pm
    HMM Topology
    Durbin et al, 68-71
    Parameter estimation, Baum-Welch algorithm
    Durbin et al, 61-71
    Ewens & Grant, 329-332
     
    21.  Nov. 9 HMMs: Modeling, parameter estimation

    Profile HMMs
    Durbin et al, 100-110
    Multiple alignment using HMMs
    Ewens & Grant, 335 - 337
     
    24.  Nov. 11 HMMs: Modeling, parameter estimation

        7Eleven assignment 4: pdf, latex, due 11:59pm, Fri, Nov 19th
    Yoon, 09


     
    23.  Nov. 16 HMM topology, Profile HMMs examples

        PS7: due 11:59pm Wed. 11/24.
        pdf, latex
    24.  Nov. 18 Multiple alignment using Profile HMMs

    7Eleven4 is due tomorrow
    Blast 1990
    - Setubal and Meidanis, 84-87 (electronic reserve)
    - Basic local alignment search tool, Altschul et al. , J. Mol. Bio., 1990 (electronic reserve)
     
    25.  Nov. 23 BLAST statistics

    PS7 is due tomorrow


    Blast statistics and data base searching:
    - The statistics of sequence similarity scores S. F. Altschul
    - Amino acid substitution matrices from an information theoretic perspective, S. F. Altschul, J. Mol. Bio., 219:555-565, 1991 (electronic reserve).
    - A protein alignment scoring system sensitive at all evolutionary distances, S. F. Altschul, J. Mol. Evol., 36:290-300, 1993 (electronic reserve).
    Protein multiple sequence alignment, Do and Katoh, 2008. (electronic reserves)
      Nov. 25 Thanksgiving Holiday: No class

        7Eleven assignment 5: pdf, due 11:59pm, Fri, Dec 3rd
    Altschul, 05
     
    26.  Nov. 30 Blast statistics


    27.  Dec. 2 Blast statistics



    Final exam Friday, Dec 10
    5:30-8:30pm

    DH1211
    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.


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    Last modified: August 31, 2021.