ScalaBLAST gives a sizeable performance
boost over BLAST, a conventional sequence
Scientists are dedicated to making discoveries that influence our world, but making these discoveries takes time. It took Albert Einstein 16 years to express his general theory of relativity. Benjamin Franklin was first introduced to electricity experiments on a trip to Boston in 1746, but his famous lightning rod experiment
didn't occur until six years later--and he knocked himself unconscious more than once in the process. Of course, Al and Ben didn't have the luxury of computing technologies and tools either. Today we have ScalaBLAST, a computational tool developed at the Pacific Northwest National Laboratory based on BLAST, a conventional sequence analysis tool developed by the National Center for Biotechnology Information (NCBI). ScalaBLAST is dramatically speeding up our understanding of the machinery of life--bringing us one step closer to curing diseases, finding safer ways to clean up the environment and protecting the country against biological threats. ScalaBLAST uses innovative high-performance computing software such as the Global Arrays Toolkit to perform sophisticated sequence alignment of proteins. Now, large-scale problems-- such as the simultaneous analysis of hundreds of organisms--can be solved in hours rather than years.
Recently, PNNL scientists completed a large-scale ScalaBLAST analysis in conjunction with the Joint Genome Institute at Lawrence Berkeley National Laboratory, solving a significant "data avalanche" problem for JGI. In just 18.5 hours, 1.6 million proteins were BLASTed against NCBI's nonredundant protein database using 1500 processors, producing 75 gigabytes of analysis results--a job that would have taken just over 3 years on a single machine.
Hold onto your seats--PNNL scientists are BLASTing us into an exciting future of scientific discovery through this and other innovations extracted from the Department of Energy Office of Advanced Scientific Computing Research Data Intensive Computing for Complex Biological Systems project. But unlike Benjamin Franklin, we won't have to knock ourselves unconscious to ride along.
The Department of Energy's Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time.