DNA Sequencing and Assembly

In this lecture, we survey a variety of different sequencing technologies, including their respective advantages and disadvantages. Then, we begin to explore the topic of genome assembly by discussing the Human Genome Project, and how genetic repeats make assembly a difficult computational task. 1 Sequencing Technologies Currently, we live in a time where genome sequencing can be done for $1,000 a person, an amazing feat, considering that the first human genome was sequencing in 2000 for over two billion dollars. This is now possible due to a variety of next generation sequencing technologies, which we will explore today. Additionally, we will discuss technologies, which while more expensive than $1,000 per person, provide much higher quality data, and overcome some shortcomings of the cheaper technologies. 1.1 Sanger Vectors Before the arrival of next generation sequencing technologies, scientists used Sanger Vectors to sequence DNA. First, DNA is fragmented into small pieces, and then inserted into a Bacterial Artificial Chromosomes (BAC). These artificial chromosomes allow the DNA to replicate, thereby producing enough DNA for gel electrophoresis. Once the DNA has been replicated to a sufficient amount, it is ready to be sequenced. Starting at the primer, the DNA chain is grown, with a supply of dideoxynucleosides. These dideoxynucleosides serve as modified As, Cs, Gs, and Ts, which end the reaction when they attach to the DNA. Since these modified nucleotides attach to the DNA fragment randomly, the reaction is stopped at all possible points in the sequence. Then, using gel electrophoresis, the products are separated to infer