An Alignment-Based Hardware Accelerator for Rapid Prediction of RNA Secondary Structures

The Zuker algorithm is a widely-adopted method for rapid prediction of RNA secondary structures. In this work, we present a new hardware architecture based on the algorithm and implement its accelerator using TSMC 40-nm technology. The proposed architecture is capable of handling more types of dangling bases when compared to the previous hardware work. Besides, with better data re-use, the idling time and memory usage of our hardware modules can be effectively reduced, and thus a higher processing speed can be achieved. Compared to the well-known software approach, RNAstructure, our 16-processing-element design has an $11\times$ speedup for RNA sequences around 3000 bases.