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Genomic Sequences Processed In Minutes, Rather Than Weeks

Date:
September 13, 2005
Source:
Pacific Northwest National Laboratory
Summary:
A new computational tool developed at the Department of Energy's Pacific Northwest National Laboratory is speeding up our understanding of the machinery of life – bringing us one step closer to curing diseases, finding safer ways to clean the environment and protecting the country against biological threats.

A new computational tool developed at the Department of Energy's Pacific Northwest National Laboratory is speeding up our understanding of the machinery of life -- bringing us one step closer to curing diseases, finding safer ways to clean the environment and protecting the country against biological threats. ScalaBLAST is a sophisticated "sequence alignment tool" that can divide the work of analyzing biological data into manageable fragments so large data sets can run on many processors simultaneously. The technology means large-scale problems -- such as the analysis of an organism -- can be solved in minutes, rather than weeks.
Credit: Image courtesy of Pacific Northwest National Laboratory

RICHLAND, WA – A new computational tool developed at the Departmentof Energy's Pacific Northwest National Laboratory is speeding up ourunderstanding of the machinery of life – bringing us one step closer tocuring diseases, finding safer ways to clean the environment andprotecting the country against biological threats.

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ScalaBLAST is a sophisticated "sequence alignment tool" that candivide the work of analyzing biological data into manageable fragmentsso large data sets can run on many processors simultaneously. Thetechnology means large-scale problems – such as the analysis of anorganism – can be solved in minutes, rather than weeks.

In the world of high-end computing, researchers assemble systemscomposed of many processors. For example, PNNL's supercomputer has1,960 processors – a big machine with lots of memory and the ability totackle large problems. However, without special modifications, softwaredoesn't run any faster on it than it would on a personal computer. Inorder to get answers to complicated biological questions more quickly,PNNL researchers "parallelized" the software using Global Arrays, apowerful programming toolkit, by creating algorithms to divvy up thework.

PNNL researchers say ScalaBLAST may be used to process complexgenomic sequences, work that is essential to understanding the buildingblocks of the genome – or rather, how they work and fit together.Genomes represent an organism's entire DNA, including its genes. Whenthe gene's sequences are analyzed they can provide clues to diseasesand possible treatments.

Using ScalaBLAST, researchers can manage the large influx of dataresulting from new questions that arise during human genome research.Prior to this new tool, it took researchers 10 days to analyze oneorganism. Now, researchers can analyze 13 organisms within nine hours,making the time-to-solution hundreds of times faster.

"Access to and understanding the pieces of genome sequences willallow researchers to understand the body's cellular machinery anddiscover clues to some types of cancer. And it will help in developingdrugs or detection methods to be used for particular diseases," saidT.P. Straatsma, a PNNL senior research scientist.

And it likely will help in other areas of human health. It's fair tosay that, in the realm of human health and disease, if you can solve aproblem in one area, you can often solve it in others – that's thenature of human biology," Straatsma said.

Having the ability to process large data sets with thiscomputational tool can also provide new insight into how microorganismscan process toxic pollutants through processes like bioremediation. Italso can help understand the components of biological systems, leadingto better detection methods for homeland security purposes and makingit possible to more quickly identify and respond to threats or developbiological countermeasures.

ScalaBLAST is a product of PNNL's Advanced Computing TechnologyLaboratory, supporting research projects associated with high-endcomputing. Development of ScalaBLAST was funded primarily by theDepartment of Energy's Office of Advanced Scientific Computing Researchas part of the BioPilot project, a larger joint research effort betweenPNNL and Oak Ridge National Laboratory.

PNNL (www.pnl.gov) is a DOE Office of Science laboratory that solvescomplex problems in energy, national security, the environment and lifesciences by advancing the understanding of physics, chemistry, biologyand computation. PNNL employs more than 4,000 staff, has a $650 millionannual budget, and has been managed by Ohio-based Battelle since thelab's inception in 1965.


Story Source:

The above story is based on materials provided by Pacific Northwest National Laboratory. Note: Materials may be edited for content and length.


Cite This Page:

Pacific Northwest National Laboratory. "Genomic Sequences Processed In Minutes, Rather Than Weeks." ScienceDaily. ScienceDaily, 13 September 2005. <www.sciencedaily.com/releases/2005/09/050911111029.htm>.
Pacific Northwest National Laboratory. (2005, September 13). Genomic Sequences Processed In Minutes, Rather Than Weeks. ScienceDaily. Retrieved October 25, 2014 from www.sciencedaily.com/releases/2005/09/050911111029.htm
Pacific Northwest National Laboratory. "Genomic Sequences Processed In Minutes, Rather Than Weeks." ScienceDaily. www.sciencedaily.com/releases/2005/09/050911111029.htm (accessed October 25, 2014).

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