DRC Computer Corp sets world record for analysing gene sequences
16 Feb 2011
DRC Computer Corporation (DRC) has achieved a world record of
9.4 trillion cell updates per second (TCUPS) and also drastically
reduced the cost of gene sequence analysis using its microprocessors and
Microsoft Windows HPC Server.
The system will enable medical researchers, pharmacologists and
DNA forensic experts to more effectively and rapidly analyze human
gene sequences to identify medical conditions, build new treatments
and complete criminal investigations.
Previously gene sequence analysis has been very costly and
lengthy, requiring expensive high performance servers. Now the time
and cost to complete can be reduced by a factor of 20 using standard
Intel-based servers installed with DRC Accelium processors and
running Microsoft Windows HPC Server 2008 R2.
Not only does this improve the analysis time but it also reduces
by over 90% the computing cost, power, real estate and
infrastructure (such as air conditioning) required to obtain the
results. Most importantly, the price/performance is over five times
better than any other published results.
"As the volume and intensity of research and commercial gene
sequence analysis increases, it is critical to have systems that can
scale to high volume analysis using standard, cost-effective
servers," commented Dr. Michael Schatz, Assistant Professor of
Quantitative Biology at Cold Spring Harbor Laboratory in the US.
“Microsoft is committed to making technical computing simpler and
more affordable for a broader audience. This world record by DRC
demonstrates the scalability of Windows HPC Server as a platform for
the most powerful algorithms and address the high performance
computing needs in the biomedical field,” said Bill Hamilton,
director in the Technical Computing group at Microsoft.
The analysis used the Smith-Waterman algorithm which is widely
used in bioscience to align DNA and protein sequences and is
considered to deliver the highest accuracy of any alignment
algorithm; however, it is computationally intensive. Using a novel
design, DRC engineers have implemented the algorithm on the
massively parallel DRC processor.
DRC achieved a performance of 9.4 trillion CUPS running 200
base-pair DNA reads against a 650,000,000 nucleotides database. This
benchmark ran on clustered, standard servers incorporating multiple
DRC processors operating as a cloud computing environment. On a
single DRC Accelium processor, DRC achieved 530 billion CUPS. DRC
used the SSEARCH35 tool within the FASTA genomics tool kit to
benchmark performance. This highly scalable architecture can extend
well beyond the configuration used in this benchmark to build a
massive cloud service capability.
“This new world record establishes that DRC processors running
the Smith-Waterman algorithm can scale to meet the most challenging
bioscience requirements,” said Mark O’Hare, DRC Chairman and CEO.
“What really surprises the experts is the outstanding