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Finding Mutations in DNA and Proteins (Bioinformatics VI)
  • Level Foundation
  • Duration 24 hours
  • Course by University of California San Diego
  • Offered by

About

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.

Modules

Welcome to Class!

    • 1 Videos
    • 1 Readings
Show info about module content

1 Videos

  • (Check Out Our Wacky Course Intro Video!)

1 Readings

  • Course Details

Week 1: How Do We Locate Disease-Causing Mutations? (Week 1/3)

    • 3 Videos
    • 1 Readings
    • 1 ExternalTool
    • 1 Assignment
Show info about module content

1 Assignment

  • How Do We Find Disease-Causing Mutations? (Week 1)

1 External Tool

  • Interactive Text for Week 1

3 Videos

  • Why Do We Map Reads?
  • Using the Trie
  • From a Trie to a Suffix Tree

1 Readings

  • Week 1 FAQs (Optional)

Complete the Code Challenges!

    • 1 ExternalTool
Show info about module content

1 External Tool

  • Open in order to Sync Your Progress: Interactive Text for Week 1

Week 2: How Do We Locate Disease-Causing Mutations? (Week 2/3)

    • 3 Videos
    • 1 Readings
    • 1 ExternalTool
Show info about module content

1 External Tool

  • Interactive Text for Week 2

3 Videos

  • String Compression and the Burrows-Wheeler Transform
  • Inverting Burrows-Wheeler
  • Using Burrows-Wheeler for Pattern Matching

1 Readings

  • Week 2 FAQs (Optional)

Complete the Code Challenges!

    • 1 ExternalTool
Show info about module content

1 External Tool

  • Open in order to Sync Your Progress: Interactive Text for Week 2

Week 3: How Do We Locate Disease-Causing Mutations? (Week 3/3)

    • 4 Videos
    • 1 Readings
    • 1 ExternalTool
    • 1 Assignment
Show info about module content

1 Assignment

  • How Do We Find Disease-Causing Mutations? (Weeks 2-3)

1 External Tool

  • Interactive Text for Week 3

4 Videos

  • Finding the Matched Patterns
  • Setting Up Checkpoints
  • Inexact Matching
  • Further Applications of Read Mapping

1 Readings

  • Week 3 FAQs (Optional)

Complete the Code Challenges on Stepic!

    • 1 ExternalTool
Show info about module content

1 External Tool

  • Open in order to Sync Your Progress: Interactive Text for Week 3

Week 4: Why Have Biologists Still Not Developed an HIV Vaccine? (Week 1/2)

    • 5 Videos
    • 1 ExternalTool
Show info about module content

1 External Tool

  • Interactive Text for Week 4

5 Videos

  • Classifying HIV Phenotypes
  • Gambling with Yakuza
  • From a Crooked Casino to a Hidden Markov Model
  • The Decoding Problem
  • The Viterbi Algorithm

Complete the Code Challenges!

    • 1 ExternalTool
Show info about module content

1 External Tool

  • Open in order to Sync Your Progress: Interactive Text for Week 4

Week 5: Why Have Biologists Still Not Developed an HIV Vaccine? (Week 2/2)

    • 5 Videos
    • 1 Readings
    • 1 ExternalTool
    • 1 Assignment
Show info about module content

1 Assignment

  • Why Have Biologists Still Not Developed an HIV Vaccine? (Weeks 4-5)

1 External Tool

  • Interactive Text for Week 5

5 Videos

  • Profile HMMs for Sequence Alignment
  • Classifying Proteins with Profile HMMs
  • Viterbi Learning
  • Soft Decoding Problem
  • Baum-Welch Learning

1 Readings

  • Week 5 FAQs (Optional)

Complete the Code Challenges!

    • 1 ExternalTool
Show info about module content

1 External Tool

  • Code Challenges for Week 5

Bioinformatics Application Challenge: HMMs for Sequence Alignment

    • 1 PeerReview
Show info about module content

1 Peer Review

  • Bioinformatics Application Challenge

Auto Summary

Explore advanced bioinformatics in "Finding Mutations in DNA and Proteins (Bioinformatics VI)," focusing on genome comparison and mutation identification. Led by Coursera, this foundational course delves into efficient combinatorial pattern matching algorithms and hidden Markov models for protein analysis. Perfect for health and fitness enthusiasts, it offers a comprehensive 1440-minute study with Starter and Professional subscription options. Ideal for those seeking to deepen their understanding of genetic sequencing and protein function amidst mutations.

Pavel Pevzner
Instructors

Pavel Pevzner

Phillip Compeau
Instructors

Phillip Compeau