Graph Algorithms in Genome Sequencing
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assignment Level : Intermediate
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Key information

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verified_user Fee-based Certificate
timer 24 hours in total

About the content

In this course, part of the Algorithms and Data Structures MicroMasters program, you will learn how graph algorithms are used in two fundamental problems in modern biology:

  • How do we sequence a genome?
  • How do we construct an evolutionary “Tree of Life?"

In the first part of the course, you will learn how genome sequencing relies on using a graph to assemble millions of tiny DNA fragments into a contiguous genome. We will then shift gears and learn how to construct an evolutionary tree of life from genome data.

  • Graph algorithms
  • Algorithms for genome assembly
  • Phylogenetics

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Prerequisite

Basic knowledge of:

  • at least one programming language: loops, arrays, stacks, recursion.
  • mathematics: proof by induction, proof by contradiction.

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Syllabus

Week 1: Introduction to Genome Sequencing and Graphs
Introduction to the basics of genome sequencing, and first attempts to model this problem using graphs.

Weeks 2 and 3: Assembling Genomes from Tiny Fragments
Applying an Eulerian path approach to assemble a genome from small pieces of DNA, and adapting this theoretical solution to practical considerations.

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Instructors

Pavel Pevzner
Ronald R. Taylor Professor of Computer Science
The University of California, San Diego

Phillip Compeau
Assistant Teaching Professor
Carnegie Mellon University

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The University of California, San Diego
The University of California, San Diego
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