High speed DNA sequencing accelerator using FPGA

Abstract

This paper presents the development of High Speed DNA sequencing accelerator based on Smith-Waterman algorithm using FPGA. The scope of the paper focuses on speed optimization with parallelism. Smith-Waterman algorithm is sensitive algorithm used for procedure of DNA sequence alignments in computational molecular biology. As the number of sequence database increase exponentially, it affects the performance of Smith-Waterman algorithm in general purpose computer. Therefore, several techniques have been developed in order to speed up the crucial sequence comparison processes. Hence, optimization technique which used parallelism approach has been utilized. Moreover, the technique, which was previously used in cluster computing, has been exploited and implemented on FPGA technology. The potential of FPGA's implementation is vast in term of cost reduction, faster speed and parallelism. The design has been described using Verilog HDL and target to Altera Cyclone II 2C70. In this paper we introduce the new technique of DNA sequencing algorithm with 10 based pair DNA sequences been aligned at single clock cycle. The result of compilation consisting of 821 logic elements with total cell delay 10.472 ns and total interconnect delays 17.592 ns.