Genome Sequencing (Bioinformatics II)

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  • Week 1: Introduction to Genome Sequencing
    • Welcome to class!

      This course will focus on two questions at the forefront of modern computational biology, along with the algorithmic approaches we will use to solve them in parentheses:

      1. Weeks 1-2: How Do We Assemble Genomes? (Graph Algorithms)
      2. How Do We Sequence Antibiotics? (Brute Force Algorithms)

      Each of the two chapters of content in the class is accompanied by a Bioinformatics Cartoon created by talented San Diego artist Randall Christopher and serving as a chapter header in the Specialization's bestselling print companion. You can find the first chapter's cartoon at the bottom of this message. What does a time machine trip to 1735, a stack of newspapers, a jigsaw puzzle, and a giant ant invading a riverside city have to do with putting together a genome? Start learning today to find out!

  • Week 2: Applying Euler's Theorem to Assemble Genomes
    • Welcome to Week 2 of class!

      This week in class, we will see how a 300 year-old mathematical theorem will help us assemble a genome from millions of tiny pieces of DNA.

  • Week 3: Sequencing Antibiotics
    • Welcome to Week 3 of class!

      This week, we begin a new chapter, titled "How Do We Sequence Antibiotics?"  In this chapter, we will learn how to determine the amino acid sequences making up antibiotics using brute force algorithms.

      Below is this week's Bioinformatics Cartoon.

  • Week 4: From Ideal to Real Spectra for Antibiotics Sequencing
    • Welcome to Week 4 of class!

      Last week, we discussed how to sequence an antibiotic peptide from an ideal spectrum. This week, we will see how to develop more sophisticated algorithms for antibiotic peptide sequencing that are able to handle spectra with many false and missing masses.

  • Week 5: Bioinformatics Application Challenge!
    • Welcome to Week 5 of class!

      This week, we will see how to apply genome assembly tools to sequencing data from a dangerous pathogenic bacterium.