Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs
ASAP '08 Proceedings of the 2008 International Conference on Application-Specific Systems, Architectures and Processors
FPGA Accelerator for RNA Secondary Structure Prediction
DSD '09 Proceedings of the 2009 12th Euromicro Conference on Digital System Design, Architectures, Methods and Tools
An experimental study of optimizing bioinformatics applications
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
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RNA secondary structure prediction, well-known like "RNA-problem", is an operation of high demand of computational resources. At present, several techniques of parallel computing are used in order to obtain efficient results to solve this problem. In this work we present the FPGA implementation of a novel and modular architecture for solution of RNA-problem. The circuit computes the minimum energy that corresponds to optimal secondary structure searched for. A parallel and pipeline design is obtained giving an O(n2) time complexity solution, in counterpart with the classic O(n3) algorithm for software implementations. We have used Xilinx FPGAs for implementations, and the packages ISE8.1i and ModelSim 6.1e respectively to make VHDL description and circuit verification.