list 6 sequences
assignment Level : Introductive
chat_bubble_outline Language : English
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Key information

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timer 24 hours in total

About the content

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.

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Syllabus

  • Week 1 - Week 1: Introduction to Sequence Alignment

    Welcome to class!

    If you joined us in the previous course in this Specialization, then you became an expert at assembling genomes and sequencing antibiotics. The next natural question to ask is how to compare DNA and amino acid sequences. T...

  • Week 2 - Week 2: From Finding a Longest Path to Aligning DNA Strings

    Welcome to Week 2 of the class!

    Last week, we saw how touring around Manhattan and making change in a Roman shop help us find a longest common subsequence of two DNA or protein strings.

    This week, we will study how to find a highest scoring ...

  • Week 3 - Week 3: Advanced Topics in Sequence Alignment

    Welcome to Week 3 of the class!

    Last week, we saw how a variety of different applications of sequence alignment can all be reduced to finding the longest path in a Manhattan-like graph.

    This week, we will conclude the current chapter by cons...

  • Week 4 - Week 4: Genome Rearrangements and Fragility

    Welcome to Week 4 of the class!

    You now know how to compare two DNA (or protein) strings.  But what if we wanted to compare entire genomes? When we "zoom out" to the genome level, we find that substitutions, insertions, and deletions don't tell...

  • Week 5 - Week 5: Applying Genome Rearrangement Analysis to Find Genome Fragility

    Last week, we asked whether there are fragile regions in the human genome. Then, we took a lengthy detour to see how to compute a distance between species genomes, a discussion that we will continue this week.

    It is probably unclear how computing th...

  • Week 6 - Week 6: Bioinformatics Application Challenge
    In the sixth and final week of the course, we will apply sequence alignment algorithms to infer the non-ribosomal code.
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Instructors

Pavel Pevzner
Professor
Department of Computer Science and Engineering

Phillip Compeau
Visiting Researcher
Department of Computer Science & Engineering

Nikolay Vyahhi
Visiting Scholar
Department of Computer Science and Engineering

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University of California, San Diego
UC San Diego is an academic powerhouse and economic engine, recognized as one of the top 10 public universities by U.S. News and World Report. Innovation is central to who we are and what we do. Here, students learn that knowledge isn't just acquired in the classroom—life is their laboratory.
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Coursera

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