An FPGA-Based Coprocessor for the Parsing of Context-Free Grammars
FCCM '00 Proceedings of the 2000 IEEE Symposium on Field-Programmable Custom Computing Machines
Faster genome annotation of non-coding RNA families without loss of accuracy
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
A Comparison of Floating Point and Logarithmic Number Systems for FPGAs
FCCM '05 Proceedings of the 13th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Integrating FPGA acceleration into HMMer
Parallel Computing
Bioinformatics
Fine-grained parallel RNA secondary structure prediction using SCFGs on FPGA
Parallel Computing
Hardware-Accelerated RNA Secondary-Structure Alignment
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
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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.