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"GREAT" Stanford tool to help researchers worldwide

Stanford researchers have developed a new, publicly available algorithm to help researchers more fully utilize the extraordinary wealth of information piling up as a result of new "deep sequencing" techniques. The intent is to help researchers broaden their search for genomic regions important in controlling the transcription of genes. The work, which was published this weekend in Nature Biotechnology, was headed up by developmental biologist and computer scientist Gill Bejerano, PhD:

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. 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.

The researchers named the web-based tool "GREAT" - for "Genomic Regions Enrichment of Annotations Tool." Scientists who log on to the site can enter a list of hundreds or thousands of DNA binding sites for control proteins called transcription factors. The tool will analyze the list and deliver an assessment of which sites affect the expression of which genes, even those separated by up to one million base pairs:

The analysis gets pushed back into the hands of the person who did the experiment...We don't expect that this tool will help three labs. We expect that it will help 3,000 labs. GREAT can look at thousands of binding sites and tell you things that your transcription factor is doing that have never been reported before.

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