COMP 342
(CRN 20538, Spring 2020)


  • Instructor: Catie Welsh
  • Office Hours: Tu/Thurs 10-11:30am, or by appointment (Briggs 208)
  • Syllabus
  • Online Textbook
  • Pass/Fail policy for course
  • Schedule

    This is a tentative schedule and subject to change as needed.

    Date Lecture Topic(s) Sections Covered Slides Assignments
    W-January 15 Introduction Chapter 1 slides Getting to Know You Survey (link on Moodle) - due by 1/17
    Read the following 2 articles: Life and Its Molecules A Brief Introduction
    Molecular Biology for Computer Scientists
    F-January 17 DNA Sequencing Technologies Chapter 3 slides Reading Assignment/Questions (paper on Moodle) (due 1/22)
    M-January 20 No Class - Holiday
    W-January 22 Exact Pattern Matching Sections 9.1-9.4 slides  
    F-January 24 Suffix Trees Section 9.5 slides Problem Set 1
    M-January 27 Knuth-Morris-Pratt
    Motif-Finding Problem
    Sections 4.4-4.9 slides  
    W-January 29 Motif Finding Algorithms Sections 4.4-4.9 slides  
    F-January 31 Greedy Motif Search Lab      
    M-February 3 Genome Rearrangements Section 5.3-5.5 slides Problem Set 2
    W-February 5 More on Genome Rearrangements Section 5.3-5.5    
    F-February 7 Dynamic Programming Intro Section 6.1-6.3    
    M-February 10 DP: Edit Distance Section 6.4    
    W-February 12 DP: LCS & Sequence Alignment Section 6.5-6.8 slides Problem Set 3
    F-February 14 Sequence Alignment Lab      
    M-February 17 Global & Local Alignment Section 6.4-6.8  
    W-February 19 Fitting Alignment & Intro to Affine Gap Penalties Section 6.9 slides  
    F-February 21 Multiple Sequence Alignment Lab Section 6.10    
    M-February 24 Alignment with Gap Penalties Section 6.9    
    W-February 26 Exam 1
    F-February 28 Space-Efficient Global Alignment & Multiple Alignment Section 7.2 and 6.10 slides  
    M-March 2 Assembling a Genome Section 8.1-8.4 slides  
    W-March 4 Overlap Graphs for SCS, Assembly terms and evaluation metrics Section 8.5 slides  
    F-March 6 Overlap-Layout-Consensus Framework for Assembly
    Assembly Worksheet
    Eulerian Cycles and Paths
    Section 8.7-8.9 slides  
    M-March 9 Spring Break - No Class
    W- March 11 Spring Break - No Class
    F-March 13 Spring Break - No Class
    M-March 16 Classes Suspended - COVID-19
    W-March 18 Classes Suspended - COVID-19
    F-March 20 Classes Suspended - COVID-19
    M-March 23 Meet via Zoom, final project details, link to recorded Zoom meeting on Moodle Read Ch. 3 (online book), Sect. 3.1-3.3   Problem Set 4 - due Friday 3/27
    Final Project Information
    Watch the following video lectures, which should be review:
    Ch. 3: String Reconstruction as a Hamiltonian Path
    Ch. 3: String Reconstruction as a Eulerian Path Problem
    Ch. 3: Similar Problems with Different Fates
    W-March 25 De Bruijn Graphs Worksheet
    Solutions for De Bruijn Worksheet
    Read Sect. 3.4-3.6 (online book) Watch these videos:
    Ch.3: De Bruijn Graphs
    Ch.3: Euler's Theorem
    F-March 27 Realities of Genome Assembly Read Sect. 3.7-3.9   Homework 5 - due Monday 4/6
    Watch these videos:
    Ch.3: Assembling Read-Pairs
    Ch.3: De Bruijn Graphs Face Harsh Realities of Assembly
    Ch.3: Konigsberg 3
    M-March 30 Which Animal Gave us SARS? Read Sect. 7.1-7.2   Watch these videos:
    Ch. 7: The Fastest Outbreak
    Ch. 7: Transforming Distance Matrices into Evolutionary Trees
    W-April 1 Phylogeny Trees Read Sect. 7.3-7.4   Project Proposal due by 11:55pm - upload to Moodle
    Watch these videos:
    Ch. 7: Towards An Algorithm for Distance-Based Phylogeny Reconstruction
    Ch. 7: Additive Phylogeny
    F-April 3 Phylogeny Trees II
    Additive Phylogeny Worksheet (Solution)
    Read Sect. 7.5-7.6   Watch these videos:
    Ch. 7: Using Least Squares to Construct Approximate Phylogenies
    Ch. 7: Ultrametric Evolutionary Trees
    M-April 6 Phylogeny Trees III
    Large Additive Phylogeny Worksheet (Solution)
    Neighbor Joining Worksheet (Solution)
    Read Sect. 7.7-7.8 Homework 6 - due Monday 4/13 Wed, 4/15
    Watch these videos:
    Ch. 7: The Neighbor-Joining Algorithm
    Ch. 7: Character-Based Tree Reconstruction
    W-April 8 The Parsimony Problem
    Notes for Sankoff and Fitch Algorithms
    Read Sect. 7.9-7.10 & Epilogue   Watch these videos:
    Ch. 7: The Small Parsimony Problem
    Ch. 7: The Large Parsimony Problem
    F-April 10 Easter Break - No Class
    M-April 13 Clustering     Watch these videos:
    Ch. 8: Clustering as an Optimization Problem
    Ch. 8: The Lloyd Algorithm for k-means Clustering
    Ch. 8: Hierarchical Clustering
    Note: all other Ch. 8 videos are optional, but recommended
    W-April 15 Work on HW and Projects     Homework 7 - due Wed, 4/22 at 2pm
    F-April 17 Work on HW and Projects      
    M-April 20 Work on HW and Projects      
    W-April 22 Optional Review Session for Exam 2
    Study Guide for Exam 2
        Presentation Details
    Presentation Grading Rubric
    F-April 24 Exam 2
    M-April 27 Project Presentations
    Fill out Course Evaluations
    Chris & Reese
    Presentation Worksheet - due 5/1 by 11:55pm
    W-April 29 Project Presentations     Aubrey & Madi
    Henry, Matthew & Addison
    John & Tim
    F-May 8 Final Project Papers due by 5:30pm - upload to Moodle