Hi, and congratulations on finishing all the courses in the specialization. Now, the only thing that stands between you and the certificate is me. Actually, it's not me. It's the capstone that I will present today. I want to explain that there are some differences between the courses you took before and this capstone. In the courses you took before, we presented you with this perfectly formulated clear algorithmic problems, that defines the range of possible parameters and the specifies the algorithms that you need, to solve this problems. In the capstone, the things will be different, the problems will be loosely defined, and you will need to transform them into exact algorithmic problems. It will not be immediately clear what is the range of the parameters, and will give you only the hint, rather than details of the algorithms that you need. However, you are now algorithmic pros, and I'm confident you will be able to solve all the challenges in this capstone. One of the biggest news in 2011 was European E coli outbreak. It started as food poisoning with bloody diarrhea, that often followed by kidney failure and death. The outbreak quickly spread from Germany to many European countries. And in the beginning it was unclear what was the cause of the outbreak. The usual suspects in the case of outbreaks are different vegetables, but which vegetables? Cucumbers, carrots, there are a lot of choices. In the beginning of the outbreak, German officials identified cucumbers as the likely source of infection. And thousand of tons of cucumbers, and other vegetables were destroyed all over Europe. Four years later, it turn out that German officials were wrong, and they were ordered to pay compensation to Spanish farmers who lost billions from destroyed cucumbers. In 2011, German house officials identified a restaurant in Lubeck where 40% of all visitors developed bloody diarrhea. After interviewing patrons of this restaurant who developed bloody diarrhea, they figure out that almost all of them ate bean sprout. The owner of this restaurants was outraged and publicly offered to eat all sprouts in his restaurants. But it turned out that the cause of the outbreak was actually a huge lot of bean sprouts that was sent from Egypt to Europe, and was now a time bomb sitting in hundreds of stores and restaurants all over the continent. In May 2011, a girl from Hamburg developed bloody diarrhea after eating sprouts, and doctors suspected that it was a common pathogenic E coli strain. But the blood sample from this girl did not pass the test for known E coli strain. At this point, it became clear that a new pathogen has emerged, and the goal was to sequence the genome of this pathogen, and to figure out how it has become pathogenic. And our goal in this capstone will be to figure out what is the genome of this mysterious E coli X from the girl admitted to a hospital room in Hamburg? To answer this question, you have to develop your own assembler and apply it for assembler grades obtained from a girl from Hamburg who developed bloody diarrhea. Developing genome assemblers is not for fainthearted. To learn more about how it is done, you may attend our Bioinformatics specialization on Coursera or read the book Bioinformatics Algorithms, An Active Learning Approach. Assembling E coli X bacterium is a rather complex algorithmic challenge. And to make it easier for you, we broke it into three simpler challenges. We start from assembling phi X174 virus, which is a small little over 5,000 nucleotide virus with just 11 genes. After wards they will assemble the smallest bacteria genome know, called N deltocephalinicola, with it's just 110 thousand nucleotides and approximately 140 genes. And finally, they will assemble 50 times 100 E coli X bacteria, which has roughly 5 million nucleotides and approximately 5,000 genes. Our first task will be to assemble a small phi X174 phage. Phages are bacterial viruses and they cannot replicate on their own and must infect bacteria to do so. And phage X174 is almost like a cult organism in genomics, because it was the first sequenced genome completed by Noble Prize winner Fred Sanger in 1977. You will follow in the footsteps of Fred Sanger to assemble the phi X174 genome. Our next task will be to assemble the smallest bacterial genome. This bacterial lives inside leafhoppers. And it's sheltered life allow it to reduce the genome to only about 110,000 nucleotides, 50 times smaller that E coli X genome. And only approximately 140 genes. It lacks some genes necessary for survival, but products of these genes are supplied by its bacterial host. And biologists believe that this bacterial genome is losing its bacterial identity and turning into part of the insect genomes. Just like mitochondria in human cells. And your goal will be to follow in the footsteps of biologists who sequenced this genome in 2013. And finally, after your sequence the phage and the smallest bacterial genomes, you will assemble E coli X.
