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New Stanford tool enables wider analyses of genome 'deep sequencing'
Date:5/2/2010

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Typically that data exists in the form of DNA binding sites for regulatory proteins called transcription factors that dictate the activity of genes. And, with the advent of new, deep-sequencing techniques, it's being generated at rates that are both unimaginable and unmanageable.

Bejerano is the senior author of the research, which will be published online May 2 in Nature Biotechnology. The researchers coined the name "GREAT" for their algorithm, an acronym for "Genomic Regions Enrichment of Annotations Tool," and the website will be available for anyone to use after May 2 at http://great.stanford.edu

There are hundreds of known transcription factors. Each controls the expression of numerous genes by binding to specific regions in the genome. This makes it difficult for scientists to know exactly how any one transcription factor is acting, particularly if it works over long stretches of DNA. Usually they'll figure out where in the DNA the protein is binding and then look for interesting genes nearby. Or, conversely, they'll find an interesting gene and look for nearby transcription-factor binding sites. But recent research has shown that sections of DNA far away can also play an important role.

It works a bit like this: Think of your kitchen. Notice all the black things. Those are your transcription-factor binding sites. But what do they do? You might figure out that sliding the lever on the toaster makes the toast pop up. And plugging it into the wall makes it get hot. But you're likely to overlook that vitally important black breaker switch on the wall behind you, or to dismiss it as inconsequential among all the other black items in the room that don't, in fact, control the toaster. That is, unless you use this new analysis.

In contrast, users of the GREAT algorithm, developed by graduate students Cory McLean and Aaron Wenger and software engineer Dave Bristor, will simply e
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Contact: Krista Conger
kristac@stanford.edu
650-725-5371
Stanford University Medical Center
Source:Eurekalert

Page: 1 2 3

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