Accelerating ncRNA homology search with FPGAs

Abstract

Over the last decade, the number of known biologically important non-coding RNAs (ncRNAs) has increased by orders of magnitude. The function performed by a specific ncRNA is partially determined by its structure, defined by which nucleotides of the molecule form pairs. These correlations may span large and variable distances in the linear RNA molecule. Because of these characteristics, algorithms that search for ncRNAs belonging to known families are computationally expensive, often taking many CPU weeks to run. To improve the speed of this search, multiple search algorithms arranged into a series of progressively more stringent filters can be used. In this paper, we present an FPGA based implementation of some of these algorithms. This is the first FPGA based approach to attempt to accelerate multiple filters used in ncRNA search. The FPGA is reconfigured for each filter, resulting in a total system speedup of 25x when compared with a single CPU.