03-511/711 Course Syllabus - Fall 2002


1.   Aug. 27 Introduction
2.   Aug. 29 Overview of computational molecular biology and genomics
3.  Sept. 3 Pairwise sequence comparison - global
PS0 handed out - due 9/12
4.   Sept. 5 The history of sequencing technology   Guest lecturer: Dr. Russell Schwartz
No office hours
5.   Sept. 10 Pairwise sequence comparison - local
6.   Sept. 12 Multiple sequence alignment - global
PS0 due in class
7.   Sept. 17 Multiple sequence alignment - global
8.   Sept. 19 Genetic Linkage and Genomic Evolution,
Science2002, registration.
Alumni Hall (formerly Masonic Temple, across 5th avenue from the Cathedral of Learning),
7th floor Auditorium.
9.   Sept. 24 Multiple sequence alignment - local
  Online protein domain databases:  
  •  CDD: Conserved Domain Database  
  •  CDART: Conserved Domain Architecture Retrieval Tool,

    PS1 handed out - due 10/1
    Alignment template
  • 10. Sept. 26 Multiple sequence alignment - local
      Hidden Markov Models (HMMs), Guest lecturer: Dr. William Cohen
    11. Oct. 1 Multiple sequence alignment - local
      HMMs continued, Guest lecturer: Dr. William Cohen
    PS1 due in class
    12. Oct. 3 Applications of HMMs to molecular biology: CpG islands, profile HMM's for modeling domains, multiple sequence alignment
    PS2 handed out - due 10/10
    Matrix template
    13. Oct. 8 Substitution matrices
      Likelihood ratios, PAM matrices
      PAM250,   BLOSUM62
    14. Oct. 10 Substitution matrices continued
      PAM and BLOSUM matrices
     Lecture outline
    PS2 due in class
    15. Oct. 15 Midterm Exam
    This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. The midterm covers all material up to and including biological applications of HMM's.
    16. Oct. 17 Review of midterm. Introduction to class projects for 03-711
    17. Oct. 22 Database searching; BLAST
      BLAST home page
     Lecture outline
    18. Oct. 24 Blast; statistics of local, ungapped alignments.
     Lecture outline
    19. Oct. 29 Gapped Blast; Blast demo.
     Lecture outline
    20. Oct. 31 Phylogeny reconstruction
     Lecture outline
      PS3 handed out - due 11/12
      Project proposal/outlines due.
    21. Nov. 5 Phylogeny reconstruction: parsimony
     Lecture outline
    22. Nov. 7 Phylogeny reconstruction: distance-based methods
     Lecture outline
    23. Nov. 12 Phylogeny reconstruction: distance-based methods
     Lecture outline
     UPGMA algorithm
     NJ algorithm
      Revised project proposal/outlines due.
      PS3 due in class
    24. Nov. 14 No class
    25. Nov. 19 Phylogeny reconstruction: maximum likelihood
     Lecture outline
     Comparison of tree reconstruction algorithms
    26. Nov. 21 Gene Finding (prokaryotic)
     Lecture outline
      PS4 handed out - due 12/03
    27. Nov. 26 Gene Finding (eukaryotic)
      Lecture outline
      Gene Prediction in the Human Genome Project
      No office hours.
      Nov. 28 Thanksgiving-no class  
    28. Dec. 3 Project presentations
      PS4 due in class
    29. Dec. 5 Project presentations
      10:30 - 10:40 Course evaluation
      Project final papers due.
    30. Monday
    Dec. 9
    Final Exam: 8:30 - 11:30 Porter Hall A18A
    This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Bring a calculator. The final exam is cummulative. You are responsible for all material covered during the semester.


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    Last modified: December 3rd, 2002.
    Maintained by Dannie Durand (durand@cs.cmu.edu).