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Genome Sequencing (Bioinformatics II) に戻る

Genome Sequencing (Bioinformatics II), カリフォルニア大学サンディエゴ校



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....


by SV

Jan 10, 2017

Great course to explore a bit of Bioinformatics for those with no background in Bioinformatics. I love the way the content has been provided, its interactivity increases the interest in the course.

by MP

Dec 08, 2017

I like the real-world tasks, especially the assembly on the final exam. Some of the programming tasks, such as the antibiotic noisy spectrum assembly, are challenging (which is good).



by Ryan Basler

May 06, 2019

Long waits for peer review....ruins what is a good course.

by Juanjo Bermudez

Apr 29, 2019

The instruction material was slightly less helpful than in bioinformatics I.

by Pinakhina Darya Vladimirovna

Apr 02, 2019

Thank you very much for such an engaging course.


Mar 25, 2019

good course!

by Lucas Miranda

Oct 09, 2018

Excellent course. I didn't have the time to follow the honor's track, but I've done it for other instances of the specialization and I can say that the interaction with Stepic works perfectly. Way to go, thank you!

by Olaf Wied

Oct 03, 2018

Great , interactive content. Well structured and explained.

by Hilda Pedraza Espitia

Aug 21, 2018

The course needs updates EXAMPLE: The version 3.0 for spades doesn't give the statistics and if you do a new version it doesn't give you the same data. I think this happened to other students, but we used Quast that it was later described in the instructions, but if it wasn't because someone suggested it in the discussion I would have follow the same path of using a new version that would have given me wrong data.

Thank you so much, This course has been helping me a lot.


by Jorge Iván Fuentes Rosado

Aug 09, 2018

good introduction :)

by Diego Jesús Martínez García

Jul 12, 2018

Great Materials but bad support

by Dr Samuel Channon-Wells

Jul 05, 2018

Another excellent course. Great to be able to start from a basic idea and keep expanding it until we look back and see we've learnt how to solve quite a complex problem!