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Researchers sequence dark matter of life
Date:9/18/2011

hers, recent studies have found, can change the way we behave by, for example, tricking us into eating more than we need. That's why it is crucial to analyze bacteria's genomes, which in turn help scientists understand bacteria's behavior.

Modern sequencing machines require DNA from one billion bacterial cells to produce a complete genome. Biologists usually grow the required amount of bacteria in cultures in the lab. That is how they obtained enough DNA to sequence E. coli. But a wide majority of bacteria99.9 percent according to some estimatescannot be cultured in the lab because they live in specific conditions and environments that are hard to reproduce, for example in symbiosis with other bacteria or on an animal's skin.

Enter Multiple Displacement Amplification (MDA) technology, developed about a decade ago by Professor Roger Lasken, now at the Venter Institute and co-author of the Nature Biotechnology study. MDA can be used on bacteria that can't be cultured in the lab. The technology is the equivalent of a copy machine that starts from a single cell and makes copies of fragments of its genome until it produces the equivalent of one billion cells. In 2005, Lasken and colleagues used MDA to sequence DNA produced from a single cell for the first time with funding from the Department of Energy.

However, while MDA is an ingenious cellular copy machine, it gives sequencing software programs a hard time. The DNA copies that MDA makes carry various errors and are not amplified uniformly: some pieces of the genome are copied thousands of times, and others only once or twice. Modern sequencing algorithms aren't equipped to deal with these disparities. In fact, they tend to discard bits of the genome that were replicated only a few times as sequencing errors, even though they could be key to sequencing the whole genome. The algorithm developed by Pevzner's team changes that. It retains these genome pieces and uses them to improve seq
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Contact: Ioana Patringenaru
ipatrin@ucsd.edu
858-822-0899
University of California - San Diego
Source:Eurekalert  

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