A hardware-based high-throughput DNA sequence alignment scheme

Abstract

An improved DNA sequence alignment scheme using a matrix named neighbouring matrix is presented in this paper. This paper also presents a simple design of the hardware implementation of the proposed global sequence alignment approach to meet the requirement of high speed processing. Additionally, this architecture efficiently uses SRAM to boost DNA sequence alignment in real time by employing a few logic circuitry for the fundamental operations of sequence alignment. The complete scheme is simulated for ten numerous cases considering sequence size ranging from 64 to 1024 nucleotides with 100 pseudo randomly generated DNA sequence pairs in each case. The proposed approach consumes almost half the time to align two DNA sequences than that of the approach based on [2]. The performance is measured in terms of Million Alignments Per Second (MAPS). The simulation result shows that the proposed scheme can align 43% — 69% more sequences than that of [2] of same DNA sequence pairs of variable lengths.