University of California San Diego
Genome Assembly Programming Challenge
University of California San Diego

Genome Assembly Programming Challenge

This course is part of Data Structures and Algorithms Specialization

Taught in English

Some content may not be translated

Neil Rhodes
Michael Levin
Michael Levin

Instructors: Neil Rhodes

41,390 already enrolled

Included with Coursera Plus

Course

Gain insight into a topic and learn the fundamentals

4.5

(322 reviews)

Advanced level
Designed for those already in the industry
17 hours (approximately)
Flexible schedule
Learn at your own pace

Details to know

Shareable certificate

Add to your LinkedIn profile

Course

Gain insight into a topic and learn the fundamentals

4.5

(322 reviews)

Advanced level
Designed for those already in the industry
17 hours (approximately)
Flexible schedule
Learn at your own pace

See how employees at top companies are mastering in-demand skills

Placeholder

Build your subject-matter expertise

This course is part of the Data Structures and Algorithms Specialization
When you enroll in this course, you'll also be enrolled in this Specialization.
  • Learn new concepts from industry experts
  • Gain a foundational understanding of a subject or tool
  • Develop job-relevant skills with hands-on projects
  • Earn a shareable career certificate
Placeholder
Placeholder

Earn a career certificate

Add this credential to your LinkedIn profile, resume, or CV

Share it on social media and in your performance review

Placeholder

There are 3 modules in this course

In April 2011, hundreds of people in Germany were hospitalized with a deadly disease that often started as food poisoning with bloody diarrhea. It was the beginning of the deadliest outbreak in recent history, caused by a mysterious bacterial strain that we will refer to as E. coli X. Within a few months, the outbreak had infected thousands and killed 53 people. To prevent the further spread of the outbreak, computational biologists all over the world had to answer the question “What is the genome sequence of E. coli X?” in order to figure out what new genes it acquired to become pathogenic. The 2011 German outbreak represented an early example of epidemiologists collaborating with computational biologists to stop an outbreak. In this Genome Assembly Programming Challenge, you will follow in the footsteps of the bioinformaticians investigating the outbreak by developing a program to assemble the genome of the deadly E. coli X strain. However, before you embark on building a program for assembling the E. coli X strain, we have to explain some genomic concepts and warm you up by having you solve a simpler problem of assembling a small virus.

What's included

2 videos4 readings1 programming assignment

DNA sequencing approach that led to assembly of a small virus in 1977 went through a series of transformations that contributed to the emergence of personalized medicine a few years ago. By the late 1980s, biologists were routinely sequencing viral genomes containing hundreds of thousands of nucleotides, but the idea of sequencing a bacterial (let alone the human) genome containing millions (or even billions) of nucleotides remained preposterous and would cost billions of dollars. In 1988, three biologists (independently and simultaneously!) came up with an idea to reduce sequencing cost and proposed the futuristic and at the time completely implausible method of DNA arrays. None of these three biologists could have possibly imagined that the implications of his own experimental research would eventually bring him face-to-face with challenging algorithmic problems. In this module you will learn about the algorithmic challenge of DNA sequencing using information about short k-mers provided by DNA arrays. You will also travel to the 18the century to learn about the Bridges of Konigsberg and solve a related problem of assembling a jigsaw puzzle!

What's included

5 videos1 programming assignment

Our discussion of genome assembly has thus far relied upon various assumptions. In this module, we will face practical challenges introduced by quirks in modern sequencing technologies and discuss some algorithmic techniques that have been devised to address these challenges. Afterwards, you will assemble the smallest bacterial genome that lives symbiotically inside leafhoppers. Its sheltered life has allowed it to reduce its genome to only about 112,091 nucleotides and 137 genes. And afterwards, you will be ready to assemble the E. coli X genome!

What's included

3 videos1 programming assignment

Instructors

Instructor ratings
4.5 (27 ratings)
Neil Rhodes
University of California San Diego
7 Courses669,544 learners

Offered by

Recommended if you're interested in Algorithms

Why people choose Coursera for their career

Felipe M.
Learner since 2018
"To be able to take courses at my own pace and rhythm has been an amazing experience. I can learn whenever it fits my schedule and mood."
Jennifer J.
Learner since 2020
"I directly applied the concepts and skills I learned from my courses to an exciting new project at work."
Larry W.
Learner since 2021
"When I need courses on topics that my university doesn't offer, Coursera is one of the best places to go."
Chaitanya A.
"Learning isn't just about being better at your job: it's so much more than that. Coursera allows me to learn without limits."

Learner reviews

Showing 3 of 322

4.5

322 reviews

  • 5 stars

    69.96%

  • 4 stars

    17.02%

  • 3 stars

    8.66%

  • 2 stars

    2.78%

  • 1 star

    1.54%

AS
5

Reviewed on Aug 4, 2018

FS
5

Reviewed on Sep 5, 2020

AG
5

Reviewed on Jul 28, 2020

New to Algorithms? Start here.

Placeholder

Open new doors with Coursera Plus

Unlimited access to 7,000+ world-class courses, hands-on projects, and job-ready certificate programs - all included in your subscription

Advance your career with an online degree

Earn a degree from world-class universities - 100% online

Join over 3,400 global companies that choose Coursera for Business

Upskill your employees to excel in the digital economy

Frequently asked questions