Software tackles protei...( CAMBRIDGE Mass. (Sept. 25 2003) When...)

CAMBRIDGE, Mass. (Sept. 25, 2003) When biologists want to compare different sequences of DNA or protein, it's as simple as plugging the information into a browser and pressing enter. Within 15 seconds, an online software tool contrasts one sequence of DNA with up to 18 million others catalogued in public databases. Now, a software tool developed by Whitehead Institute scientists promises to apply this same computational muscle to the far more intricate world of protein interaction networks, giving researchers a new view of the complexities of cellular life.

DNA sequencing technologies allow scientists to easily identify genes and their nucleotide building blocks -- linear strings of information represented by the letters A, C, T and G. The wide accessibility of these technologies has enabled both companies and academic labs to assemble huge libraries of genomic information. Computer engineers, in turn, have helped scientists navigate these oceans of data through tools such as BLAST, the primary software platform that scientists use to compare protein and DNA sequences. However, many researchers believe that the next phase of genomics research will be to map out interaction networks -- the cell's internal wiring system through which genes and proteins communicate.

"The 80s and 90s were about sequences," says Trey Ideker, a former Whitehead Fellow who recently was named an assistant professor of bioengineering at University of California, San Diego. "Now we're starting to see newer types of technologies -- like microarrays -- that allow us to look at how a cell, in its entirety, responds to drugs and other kinds of stimuli. These technologies will revolutionize biology." Already, researchers like Whitehead's Rick Young are beginning to assemble libraries of cellular network pathway maps using microarrays.

"But there's a problem that's not yet addressed," says Whitehead Fellow Brent Stockwell. "What if I've identified a whole protein interact
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Contact: Kelli Whitlock or David Cameron
newsroom@wi.mit.edu
617-258-5183
Whitehead Institute for Biomedical Research
25-Sep-2003

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