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Genomic Projects Genome Projects Genome projects are scientific endeavours that aim to map the genome of a living being or of a species (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus), that is, the complete set of genes caried by this living being or virus. The Human Genome Project was such a project. Some have argued that the era of genomics is one of the more fundamental advances in human history. Genome sequencing There are essentially two ways to sequence a genome. The BAC-to-BAC method, the first to be employed in human genome studies, is slow but sure. The BAC-to-BAC approach, also referred to as the map-based method, evolved from procedures developed by a number of researchers during the late 1980s and 90s and that continues to develop and change.* The other technique, known as whole genome shotgun sequencing, brings speed into the picture, enabling researchers to do the job in months to a year. The shotgun method was developed by J. Craig Venter in 1996. 1.BAC to BAC Sequencing The BAC to BAC approach first creates a crude physical map of the whole genome before sequencing the DNA. Constructing a map requires cutting the chromosomes into large pieces and figuring out the order of these big chunks of DNA before taking a closer look and sequencing all the fragments. 1.Several copies of the genome are randomly cut into pieces base pairs (bp) long. 2.Each of these fragments is inserted into a BAC-a bacterial artificial chromosome. A BAC is a man made piece of DNA that can replicate inside a bacterial cell. The whole collection of BACs containing the entire human genome is called a BAC library, because each BAC is like a book in a library that can be accessed and copied. 3.These pieces are fingerprinted to give each piece a unique identification tag that determines the order of the fragments. Fingerprinting involves cutting each BAC fragment with a single enzyme and finding common sequence landmarks in overlapping fragments that determine the location of each BAC along the chromosome. Then overlapping BACs with markers every 100,000 bp form a map of each chromosome. All the M13 libraries are sequenced. 500 bp from one end of the fragment are sequenced generating millions of sequences.These sequences are fed into a computer program called PHRAP that looks for common sequences that join two fragments together. 2.Whole Genome Shotgun Sequencing The shotgun sequencing method goes straight to the job of decoding, bypassing the need for a physical map. Therefore, it is much faster. 1.Multiple copies of the genome are randomly shredded into pieces that are 2,000 base pairs (bp) long by squeezing the DNA through a pressurized syringe. This is done a second time to generate pieces that are 10,000 bp long. 2.Each 2,000 and 10,000 bp fragment is inserted into a plasmid, which is a piece of DNA that can replicate in bacteria. The two collections of plasmids containing 2,000 and 10,000 bp chunks of human DNA are known as plasmid libraries. 3.Both the 2,000 and the 10,000 bp plasmid libraries are sequenced. 500 bp from each end of each fragment are decoded generating millions of sequences. Sequencing both ends of each insert is critical for the assembling the entire chromosome. Computer algorithms assemble the millions of sequenced fragments into a continuous stretch resembling each chromosome.
Reference: 1. Burke, D.T. et al . Cloning of large segments of exogenous DNA into yeast by means of artificial chromosomal vectors. Science 236 , 806-812 (1987).
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