Abstract:

Noncoding RNAs have important functional roles in biological processes and become a central research interest in modern molecular biology. QRNA is one of the  powerful programs and has been widely used as an efficient analysis tool to detect the ncRNA gene at present. Unfortunately, the O(〖WTBX〗L〖WTBZ〗3) computing requirements and complicated data dependency greatly limit the usefulness of the QRNA package with the explosion in gene databases. In this paper, we present a finegrained parallel QRNA prototype system for accelerating the ncRNA gene detection application on the FPGA chip. The experimental results show a factor of more than 18x speedup over the QRNA2.0.3c software running on a PC platform with the AMD Phenom 9650 Quad CPUs for pairwise sequence alignments with 996 bps, however the power consumption of our FPGA accelerator is only about 20% of the of the latter.

Key words: bioinformatics;noncoding RNA;finegrained parallelism;hardware accelerator;FPGA