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

STANFORD, Calif. - Life is almost unbearably complex. Humans and mice, frogs and flies toggle genes on and off in dizzying combinations and sequences during their relentless march from embryo to death. Now scientists seeking to understand the machinations of the proteins behind the genomic wizard's screen have a powerful new tool at their disposal, courtesy of researchers at the Stanford University School of Medicine.

Until now, researchers have relied on outdated methods of analysis to identify those DNA sequences involved in controlling when and how individual genes are expressed. Most often, those methods - capable of probing only specific, limited regions of the genome arising from a type of experiment called DNA microarrays - led to the exclusive scrutiny of regions called promoters nestled near the start of the gene.

In contrast, the new Stanford-developed, web-based algorithm allows scientists to plumb the unprecedented depths of the data provided by new "deep-sequencing" techniques to reveal a pantheon of control regions for nearly any gene. The effect is like expanding a researcher's field of vision from a pencil-thin beam of light trained mainly on the regions near coding sequences to a sweeping spotlight illuminating the contributions of distant genomic regions.

"It used to be that people thought only the regions near the gene were important in controlling its function - in part because they had no way of assessing the impact of regions further away," said Gill Bejerano, PhD, assistant professor of developmental biology and of computer science at the medical school and Stanford's School of Engineering.

As a result, said Bejerano, researchers often cherry-picked nearby regions for further analysis based on their proximity or interest. "But when you're being that conservative with current sequencing capabilities, you're typically throwing away at least half of the data you so laboriously worked to obtain," he said.'/>"/>

Contact: Krista Conger
kristac@stanford.edu
650-725-5371
Stanford University Medical Center
Source:Eurekalert

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