FPGA Accelerator for RNA Secondary Structure Prediction

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 the prototype of an accelerating circuit 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(n) 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.