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Finding Mutations in DNA and Proteins (Bioinformatics VI)

Approx. 24 hours to complete

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Course Summary

Learn about DNA mutations and their impact on human health and disease with this introductory course. Discover the latest research and techniques used in the field of genetics.

Key Learning Points

Explore the different types of DNA mutations and their effects on gene expression.
Understand how mutations can lead to genetic diseases and cancer.
Learn about the latest tools and techniques used in genetic research.

Learning Outcomes

Understand the different types of DNA mutations and their effects on gene expression.
Learn how mutations can lead to genetic diseases and cancer.
Become familiar with the latest tools and techniques used in genetic research.

Prerequisites or good to have knowledge before taking this course

Basic knowledge of biology and genetics.
Access to a computer and the internet.

Course Difficulty Level

Intermediate

Course Format

Online
Self-paced

Similar Courses

Genetics and Society
Introduction to Bioinformatics
Molecular Biology

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Description

In previous courses in the Specialization, we have discussed how to sequence and compare genomes. This course will cover advanced topics in finding mutations lurking within DNA and proteins.

In the first half of the course, we would like to ask how an individual's genome differs from the "reference genome" of the species. Our goal is to take small fragments of DNA from the individual and "map" them to the reference genome. We will see that the combinatorial pattern matching algorithms solving this problem are elegant and extremely efficient, requiring a surprisingly small amount of runtime and memory. In the second half of the course, we will learn how to identify the function of a protein even if it has been bombarded by so many mutations compared to similar proteins with known functions that it has become barely recognizable. This is the case, for example, in HIV studies, since the virus often mutates so quickly that researchers can struggle to study it. The approach we will use is based on a powerful machine learning tool called a hidden Markov model. Finally, you will learn how to apply popular bioinformatics software tools applying hidden Markov models to compare a protein against a related family of proteins.

Outline

Week 1: Introduction to Read Mapping
(Check Out Our Wacky Course Intro Video!)
Why Do We Map Reads?
Using the Trie
From a Trie to a Suffix Tree
Course Details
How Do We Find Disease-Causing Mutations? (Week 1)

Week 2: The Burrows-Wheeler Transform
String Compression and the Burrows-Wheeler Transform
Inverting Burrows-Wheeler
Using Burrows-Wheeler for Pattern Matching

Week 3: Speeding Up Burrows-Wheeler Read Mapping
Finding the Matched Patterns
Setting Up Checkpoints
Inexact Matching
Further Applications of Read Mapping
How Do We Find Disease-Causing Mutations? (Weeks 2-3)

Week 4: Introduction to Hidden Markov Models
Classifying HIV Phenotypes
Gambling with Yakuza
From a Crooked Casino to a Hidden Markov Model
The Decoding Problem
The Viterbi Algorithm

Week 5: Profile HMMs for Sequence Alignment
Profile HMMs for Sequence Alignment
Classifying Proteins with Profile HMMs
Viterbi Learning
Soft Decoding Problem
Baum-Welch Learning
Why Have Biologists Still Not Developed an HIV Vaccine? (Weeks 4-5)

Week 6: Bioinformatics Application Challenge

Summary of User Reviews

Discover how DNA mutations occur and how they can lead to genetic diseases. This course is highly recommended by students who found it informative and engaging. One key aspect that many users thought was good is the use of real-life examples to explain complex concepts.

Pros from User Reviews

Well-structured content that is easy to understand
Engaging lectures with real-life examples
Great course for beginners and experts alike
Excellent resources for further learning

Cons from User Reviews

Lack of interaction with course instructors
Some technical difficulties with video lectures
Not enough practice questions
Lack of peer interaction

Recommended for you

Finding Mutations in DNA and Proteins (Bioinformatics VI)

In previous courses in the Specialization, we have discussed how to sequence and compare genomes. This course will cover advanced topics in finding mutations lurking within DNA and proteins....

Save Course