TOOLS: Finding the Fly's Switches

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Science  15 Feb 2002:
Vol. 295, Issue 5558, pp. 1199
DOI: 10.1126/science.295.5558.1199c

If you've fumbled for the light switch in a dark room, you know how molecular biologists feel when they search for enhancers, small stretches of DNA that control genes. These regulatory regions, which bind proteins called transcription factors, are not always where you'd expect them to be—adjacent to the genes they flick on. The 2-month-old Fly Enhancer Web site makes it easier to find these elusive sequences in the Drosophila genome.

University of Chicago graduate student Michele Markstein designed the site with her parents, who are computer scientists, and colleague Ka-Ping Yee. Conventional genome- scanning tools such as BLAST often overlook these snippets of DNA, says Markstein, but Fly Enhancer can simultaneously search for up to 10 different sequences as small as four nucleotides each. The output specifies each potential enhancer's location and the identities of nearby genes that it might regulate. Markstein says the site had been up for only a few hours when she got the first request for a version to screen the genomes of other model organisms. She plans to post similar search tools for the nematode and for Arabidopsis.

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