Comparing Genes, Proteins, and Genomes (Bioinformatics III)
About the course
DNA mutations can broadly be divided into two categories. Point mutations, in which a single nucleotide (A, C, G, T) is altered, inserted, or deleted, are comparable to erosion slowly changing the shape of a boulder. Much of human differentiation is attributable to the accumulation of point mutations.
The other type of mutation is extremely rare and can cause dramatic effects on the scale of species evolution. In genome rearrangements, huge blocks of DNA are heaved around, often from one chromosome to another. These mutations are comparable to earthquakes, which hoist up mountains and wrench apart continents.
When we compare two relatively short pieces of DNA that have not been affected by genome rearrangements (say, two genes taken from individuals from the same species), our goal is to identify a "path of least resistance" connecting these two genes via point mutations. We can find such a path using a powerful algorithmic paradigm called dynamic programming.
On the other hand, when we zoom out to the compare entire genomes taken from different species that diverged millions of years ago (such as humans and mice), the effects of genome rearrangements become more pronounced. To determine how far diverged these genomes are, we will need completely different combinatorial algorithms that will help us answer questions about the patterns of genome rearrangements. For example, in order to move around large blocks of DNA, a genome rearrangement must "break" the genome in at least two places. We know that there are fault lines on the earth's surface where earthquakes are more likely; are there analogous "fragile regions" in the human genome where breakage has been more likely to occur during a genome rearrangement?
The Bioinformatics Specialization to which this class belongs covers exactly the same material as the core bioinformatics class in the "Bioinformatics and Systems Biology" program at the University of California at San Diego, one of the top bioinformatics programs in the world. In other words, you will have exactly the same lectures and homework assignments as students at UCSD. Moreover, many leading universities have adopted this material in their offline classes. Our goal is to provide you with the same high-quality materials that these students study in their offline classes.