A Hybrid Heuristic/Deterministic Dynamic Programing Technique for Fast Sequence Alignment

Abstract

Dynamic programming seeks to solve complex problems by breaking them down into multiple smaller problems. The solutions of these smaller problems are then combined to reach the overall solution. Deterministic algorithms have the advantage of accuracy but they need large computational power requirements. Heuristic algorithms have the advantage of speed but they provide less accuracy. This paper presents a hybrid design of dynamic programing technique that is used for sequence alignment. Our technique combines the advantages of deterministic and heuristic algorithms by delivering the optimal solution in suitable time. we implement our design on a Xilinx Zynq-7000 Artix-7 FPGA and show that our implementation improves the performance of sequence alignment by 63% for in comparison to the traditional known methods.

Heterogeneous HW/SW FPGA-Based Embedded System for Database Sequencing Applications

“…Powerful and efficient techniques have been suggested to compute these huge amounts of data in a more realistic time using the FPGAs [12], [13]. The authors of [14] proposed a Recursive Variable Expansion (RVE) based technique and implemented it on the FPGA.…”