Genome boost in Washington

Collaboration between researchers at the University of Washington and Pico Computing has yielded up to 90-fold acceleration of Infernal, a software package commonly used to identify non-coding ribonucleic acid (ncRNA). Infernal can take upwards of a few weeks to complete on commodity CPUs. However, with Pico’s FPGA accelerated solution, this identification process has been reduced to less than a day, resulting in an up to 90-fold improvement.

In the traditional model of molecular biology, DNA is transcribed to form RNA, which in turn is translated into proteins. These proteins perform many of the functions essential to biological life. In recent decades, biologists have come to understand the importance of ncRNAs, which directly perform roles normally associated with proteins including regulating genes and catalysing reactions. Further study of ncRNA may result in breakthroughs in the areas such as cancer, Alzheimer’s, and Parkinson’s disease. 

In the past 10 years, the number of modelled ncRNA families identified has increased by two orders of magnitude. Many ncRNA's bases have purely structural roles requiring two potentially distant bases to be complementary. This makes the search for ncRNA more difficult than traditional DNA sequence matching. Growth of these ncRNA families as well as computational complexity of searching genomes for known ncRNA has resulted in runtimes on the order of weeks.

Researchers at the University of Washington, using Pico’s M-503 FPGA module, have accelerated algorithms within Infernal. This implementation yielded individual algorithm speedups of up to 200-fold, for an overall software acceleration of up to 90-fold.

'The last decade of genome research has yielded a flood of novel non-protein-coding RNAs (ncRNAs) with diverse biological functions, and tantalizing hints of thousands more. Pico's hardware has enabled us to reach new levels of acceleration for key computationally intensive algorithms needed to fully explore this important new landscape,' said Dr Walter L. Ruzzo, professor at the university.

Twitter icon
Google icon icon
Digg icon
LinkedIn icon
Reddit icon
e-mail icon
Analysis and opinion

Robert Roe investigates some of the European projects focusing on preparing today’s supercomputers and HPC programmers for exascale HPC


The Jülich Supercomputing Centre (JSC) at Forschungszentrum Jülich in Germany has been operating supercomputers of the highest performance class since 1987. Tim Gillett talks to Norbert Attig and Thomas Eickermann


Gemma Church investigates how simulation and modelling de-risks the detection and extraction of geothermal energy resources


Robert Roe investigates the importance of upgrading legacy laboratory informatics systems and the benefits this provides to scientists