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Comparing Genes, Proteins, and Genomes (Bioinformatics III)
  • Level Foundation
  • المدة 22 ساعات hours
  • الطبع بواسطة University of California San Diego
  • Offered by

عن

Once we have sequenced genomes in the previous course, we would like to compare them to determine how species have evolved and what makes them different. In the first half of the course, we will compare two short biological sequences, such as genes (i.e., short sequences of DNA) or proteins. We will encounter a powerful algorithmic tool called dynamic programming that will help us determine the number of mutations that have separated the two genes/proteins. In the second half of the course, we will "zoom out" to compare entire genomes, where we see large scale mutations called genome rearrangements, seismic events that have heaved around large blocks of DNA over millions of years of evolution. Looking at the human and mouse genomes, we will ask ourselves: just as earthquakes are much more likely to occur along fault lines, are there locations in our genome that are "fragile" and more susceptible to be broken as part of genome rearrangements? We will see how combinatorial algorithms will help us answer this question. Finally, you will learn how to apply popular bioinformatics software tools to solve problems in sequence alignment, including BLAST.

الوحدات

Welcome to Class!

    • 1 Videos
    • 1 Readings
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1 Videos

  • (Check Out Our Wacky Course Intro Video!)

1 Readings

  • Course Details

Week 1: How Do We Compare Biological Sequences? (Part 1/3)

    • 6 Videos
    • 1 Readings
    • 1 ExternalTool
    • 1 Assignment
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1 Assignment

  • Week 1 Quiz

1 External Tool

  • Interactive Text for Week 1

6 Videos

  • From Sequence Comparison to Biological Insights
  • The Alignment Game and the Longest Common Subsequence Problem
  • The Manhattan Tourist Problem
  • The Change Problem
  • Dynamic Programming and Backtracking Pointers
  • From Manhattan to the Alignment Graph

1 Readings

  • Week 1 FAQs (Optional)

Complete the Code Challenges!

    • 1 ExternalTool
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1 External Tool

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

Week 2: How Do We Compare Biological Sequences? (Part 2/3)

    • 1 Videos
    • 1 Readings
    • 1 ExternalTool
    • 1 Assignment
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1 Assignment

  • Week 2 Quiz

1 External Tool

  • Interactive Text for Week 2

1 Videos

  • From Global to Local Alignment

1 Readings

  • Week 2 FAQs (Optional)

Complete the Code Challenges!

    • 1 ExternalTool
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1 External Tool

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

Week 3: How Do We Compare Biological Sequences? (Part 3/3)

    • 3 Videos
    • 1 Readings
    • 1 ExternalTool
    • 1 Assignment
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1 Assignment

  • Week 3 Quiz

1 External Tool

  • Interactive Text for Week 3

3 Videos

  • Penalizing Insertions and Deletions in Sequence Alignment
  • Space-Efficient Sequence Alignment
  • Multiple Sequence Alignment

1 Readings

  • Week 3 FAQs (Optional)

Complete the Code Challenges!

    • 1 ExternalTool
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1 External Tool

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

Week 4: Are There Fragile Regions in the Human Genome? (Part 1/2)

    • 5 Videos
    • 1 Readings
    • 1 ExternalTool
    • 1 Assignment
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1 Assignment

  • Week 4 Quiz

1 External Tool

  • Interactive Text for Week 4

5 Videos

  • Transforming Men Into Mice
  • Sorting by Reversals
  • Breakpoint Theorem
  • Rearrangements in Tumor Genomes
  • 2-Breaks

1 Readings

  • Week 4 FAQs (Optional)

Complete the Code Challenges!

    • 1 ExternalTool
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1 External Tool

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

Week 5: Are There Fragile Regions in the Human Genome?

    • 4 Videos
    • 1 Readings
    • 1 ExternalTool
    • 1 Assignment
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1 Assignment

  • Week 5 Quiz

1 External Tool

  • Interactive Text for Week 5

4 Videos

  • Breakpoint Graphs
  • 2-Break Distance Theorem
  • Rearrangement Hotspots in the Human Genome
  • Synteny Block Construction

1 Readings

  • Week 5 FAQs (Optional)

Complete the Code Challenges!

    • 1 ExternalTool
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1 External Tool

  • Open in order to Sync Your Progress: Interactive Text for Week 5

Bioinformatics Application Challenge: Sequence Alignment

    • 1 PeerReview
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1 Peer Review

  • Bioinformatics Application Challenge

Auto Summary

Explore the fascinating world of bioinformatics with "Comparing Genes, Proteins, and Genomes." This course delves into genome sequencing, comparing biological sequences, and understanding evolutionary differences. Led by expert instructors, you'll learn dynamic programming, analyze genome rearrangements, and apply bioinformatics tools like BLAST. Ideal for foundational learners in health and fitness, the course spans 1320 minutes and offers Starter and Professional subscription options. Perfect for those interested in genetics and evolutionary biology.

Pavel Pevzner
Instructors

Pavel Pevzner

Phillip Compeau
Instructors

Phillip Compeau

Nikolay Vyahhi
Instructors

Nikolay Vyahhi