Pico Computing Demonstrates Bioinformatics Acceleration at SC 2011

Seattle, WA (PRWEB) November 09, 2011

Pico Computing will be demonstrating an FPGA implementation of BFAST resulting in a 350X acceleration over a softwareonly implementation running on two quad core Intel Xeon processors. The 350X acceleration was achieved using 8 Pico M-503 FPGA modules in their SC5 SuperCluster chassis. The BFAST algorithm is primarily used in short read genome mapping.

The study of DNA has become computationally intensive to due to rapid improvements in both cost and throughput of next-generation sequencing machines. Scientists use these next-generation sequencing machines to replicate a DNA strand many times, randomly cut strands into short lengths, sequence the nucleotide bases of each length, and then compare against a known reference genome.

Next-generation sequencing machines are able to sequence the short pieces of DNA, which are called short reads, in a massively parallel fashion, leading to lower cost per genome and higher throughput per run. However, the process of mapping those short reads to a reference genome relies on software programs to search the three billion base-pair genome for places where each short read appears. The time required to complete this mapping phase is becoming the bottleneck for DNA studies, since CPUs are not able to exploit the inherent data parallelism in the search.

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Ibrar Ayyub

Ibrar Ayyub is an experienced technical writer with a Master's degree in computer science from BZU Multan University. He has written for various industries, mainly home automation, and engineering. He has a clear and simple writing style and is skilled in using infographics and diagrams. He is a great researcher and is able to present information in a well-organized and logical manner.

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