From 2010.igem.org

Introduction: presentation of our project

As part of our iGEM 2010 project, we are implementing the draft Government guidance for sequence screening, characterizing its performance, and suggesting improvements. Our findings not only quantify the Government guidance for the first time, but also should help to provide future developers of screening software with the data necessary to develop more robust sequence screening tools. Our work has direct implications for both iGEM and the field of synthetic biology.

Gene synthesis technology gives scientists an unparalleled capability to manipulate genomes. Over the past several decades, an entire commercial industry has developed to inexpensively produce genes on a large scale. It is this industry which provides the genes and standardized parts to make synthetic biology, and iGEM, possible.

Synthetic genomics, like synthetic biology, has the potential to be both a great benefit and a great detriment to public health and national security. A precedence for the dual use of synthetic genomics is the reconstruction of the virus responsible for the pandemic 1918 Spanish Flu in 2005 by researchers at the CDC (See more). Although this virus's genes were synthesized for legitimate research purposes, they could have just as easily been used to reconstructed a biological weapon. Although such engineering is difficult at the moment, advances in this technology over the next decade could make it easier for bioterrorists to harm the Public (Garfinkel et al. 2007). According to a 2004 report by the U.S. National Intelligence Council, its greatest security concern over the coming years is that terrorists will acquire biological agents for use as weapons of mass destruction (NIC, 2004).

Many genes encoding for or derived from dangerous toxins or pathogens can be freely accessed on the U.S. National Center for Biotechnology Information GenBank (NCBI-GenBank). The ease with which dangerous sequences can be located and synthesized presents novel threats to both public health and national security. To prevent illicit activities by end users of de novo synthesized genes, it is crucial to stop their manufacture at the source: gene synthesis companies. Therefore, effective and efficient screening measures must be developed to identify sequences of concern within a synthesis order.

The United States government recognizes its responsibility to protect the public and in November, 2009, published a draft guidance for sequence screening. As part of our iGEM 2010 project, we are implementing the draft Government guidance for sequence screening, characterizing its performance, and suggesting improvements.

iGEM attempts to develop a tool-box of standardized parts for use by synthetic biologists. Without screening software, dangerous sequences could find their way into the tool-box. If such sequences were ordered and transformed into, the repercussions could be significant. Our work could therefore play an integral role in both the future of the competition and the field.

Who are we?

We are a software team, composed by 5 students (2 from ENSIMAG and 3 from Virginia Tech) working in the Virginia Bioinformatics Institut, under the supervision of Jean Peccoud and with Laura Adam as advisor. The team is more thoroughly presented in Our team.

project overview

References

Annexes

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