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FPGA Cluster Accelerates Bioinformatics Application by 5000X



Pico Computing claims that it has achieved greater than 5000X acceleration of a bioinformatics sequence analysis and dot plot algorithm using a cluster of 112 commodity FPGA devices.

DNA sequencing and analysis are indispensable in basic research as well as in pharmaceutical development, disease prevention, and criminal forensics. A dot plot, also called a "matrix plot," is a graphical tool for visualization enabling the comparison of two DNA sequences. A dot plot provides an easy way to understand a large amount of information about the relationship of two sequences, and serves as a framework for further analysis.

"The dot plot algorithm is an excellent example of how a scalable FPGA platform can speed the development and deployment of complex algorithms," said Greg Edvenson, Senior Software Engineer at Pico Computing and the developer of the accelerated bioinformatics application. "I was able to optimize and debug the core algorithm using a single, modestly-sized FPGA device, then scale to multiple FPGAs to achieve the desired levels of performance. This approach greatly reduced the overall development time."

The FPGA-accelerated dot plot algorithm, written C, performs sequence analysis and pair-match scoring of DNA runs with lengths of 25 base pairs. The algorithm is inherently parallel, making it an ideal candidate for acceleration using large number of FPGA devices.

Edvenson used a single FPGA device during initial algorithm development. The FPGA was encapsulated in a Pico Computing E-17 card attached directly to a laptop computer via an ExpressCard interface. After the algorithm was tested and working as a single hardware process, Edvenson then scaled up and replicated the algorithm for deployment on the FPGA cluster. C-to-FPGA tools provided by Impulse Accelerated Technologies were used during the development of the algorithms, reducing the need to write low-level HDL code.

"There are many advantages to using scalable clusters of lower-cost, power-efficient Spartan FPGAs for cluster computing," said Dr. Robert Trout, Pico Computing Founder and CEO. "This approach reduces the overall cost per computation, and it also speeds development times because the FPGA placement and routing for each FPGA runs much faster than when working with larger, higher-density FPGA devices."

Pico Computing specializes in highly integrated development and deployment platforms based on Field Programmable Gate Array (FPGA) technologies. Applications for Pico Computing technologies include cryptography, networking, signal processing, bioinformatics, and scientific computing. Pico Computing products are used in embedded systems as well as in military, national security and high-performance computing applications.


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