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Genome Sequencing (Bioinformatics II)

Approx. 17 hours to complete

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Course Summary

In this course, you will learn about genome sequencing, including the technologies used, the data generated, and the computational methods required to analyze and interpret the data.

Key Learning Points

Understand the principles and technologies behind genome sequencing
Learn about the data generated from genome sequencing
Gain an understanding of the computational methods required to analyze and interpret genome sequencing data

Learning Outcomes

Understand the principles and technologies behind genome sequencing
Learn about the data generated from genome sequencing
Gain an understanding of the computational methods required to analyze and interpret genome sequencing data

Prerequisites or good to have knowledge before taking this course

Basic knowledge of biology and genetics
Basic programming skills

Course Difficulty Level

Intermediate

Course Format

Online
Self-paced

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Description

You may have heard a lot about genome sequencing and its potential to usher in an era of personalized medicine, but what does it mean to sequence a genome?

Biologists still cannot read the nucleotides of an entire genome as you would read a book from beginning to end. However, they can read short pieces of DNA. In this course, we will see how graph theory can be used to assemble genomes from these short pieces. We will further learn about brute force algorithms and apply them to sequencing mini-proteins called antibiotics. In the first half of the course, we will see that biologists cannot read the 3 billion nucleotides of a human genome as you would read a book from beginning to end. However, they can read shorter fragments of DNA. In this course, we will see how graph theory can be used to assemble genomes from these short pieces in what amounts to the largest jigsaw puzzle ever put together. In the second half of the course, we will discuss antibiotics, a topic of great relevance as antimicrobial-resistant bacteria like MRSA are on the rise. You know antibiotics as drugs, but on the molecular level they are short mini-proteins that have been engineered by bacteria to kill their enemies. Determining the sequence of amino acids making up one of these antibiotics is an important research problem, and one that is similar to that of sequencing a genome by assembling tiny fragments of DNA. We will see how brute force algorithms that try every possible solution are able to identify naturally occurring antibiotics so that they can be synthesized in a lab. Finally, you will learn how to apply popular bioinformatics software tools to sequence the genome of a deadly Staphylococcus bacterium that has acquired antibiotics resistance.

Outline

Week 1: Introduction to Genome Sequencing
(Check Out Our Wacky Course Intro Video!)
FIELD TRIP!
What Is Genome Sequencing?
Exploding Newspapers
The String Reconstruction Problem
String Reconstruction as a Hamiltonian Path Problem
String Reconstruction as an Eulerian Path Problem
Similar Problems with Different Fates
Course Details
Week 1 Quiz

Week 2: Applying Euler's Theorem to Assemble Genomes
De Bruijn Graphs
Euler's Theorem
Assembling Read-Pairs
De Bruijn Graphs Face Harsh Realities of Assembly
Returning to Konigsberg
Week 2 Quiz

Week 3: Sequencing Antibiotics
The Discovery of Antibiotics
How Do Bacteria Make Antibiotics?
Sequencing Antibiotics by Shattering Them into Pieces
A Brute Force Algorithm for Cyclopeptide Sequencing
Cyclopeptide Sequencing with Branch and Bound
Week 3 Quiz

Week 4: From Ideal to Real Spectra for Antibiotics Sequencing
Adapting Sequencing for Spectra with Errors
From 20 to More than 100 Amino Acids
The Spectral Convolution Saves the Day
The Truth About Spectra
Week 4 Quiz

Week 5: Bioinformatics Application Challenge!

Summary of User Reviews

Discover the fascinating world of genome sequencing with this comprehensive course on Coursera. Users have praised the course for its engaging content and knowledgeable instructors.

Key Aspect Users Liked About This Course

The course is praised for its in-depth coverage of genome sequencing techniques and technologies.

Pros from User Reviews

The course offers a great foundation for those interested in genome sequencing.
The instructors are knowledgeable and engaging.
The course is well-structured and easy to follow.
The course provides hands-on experience with genome sequencing tools.
The course offers a certificate of completion.

Cons from User Reviews

Some users found the content to be too basic.
Some users experienced technical issues with the course platform.
The course may not be suitable for those without a background in biology.
The course may not be engaging enough for those with advanced knowledge in the field.
The course may require additional resources to fully understand the content.

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