UCSD Jacobs School of Engineering University of California San Diego
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Genomics Tools
Software Maps Protein Pathways

H. pylori, on the left, contains 1,465 interaction networks, compared with S. cerevisiae’s 14,489. In just a few seconds, PathBLAST used these pathway maps to identify all networks common to both species.

When biologists want to compare sequences of DNA, it’s as simple as plugging the information into a browser and pressing 'enter'. In seconds, a software tool contrasts one sequence with up to 18 million others in public databases. Now, Jacobs School bioengineering professor Trey Ideker and his colleagues at the Whitehead Institute are applying this same computational muscle to protein interaction networks - the cell’s system through which genes and proteins communicate.

The new software tool, called PathBLAST (www.pathblast.org), represents protein interaction networks based on algorithms used to represent chemical structures. Ideker and Whitehead Fellow Brent Stockwell recently used PathBLAST to contrast the interaction networks in the yeast S. cerevisiae and the bacterium H. pylori. The study revealed that one pathway critical in DNA replication and another one instrumental in protein degradation were conserved in both organisms as a single network. Ideker says as labs continue to do these types of experiments, there could eventually be a huge payoff in comparing such things as viral networks to human networks, possibly allowing drug companies to develop products that target cellular pathways unique to viruses.