A novel design on faster processing of DNA sequences base on pipelined structure has been presented in this paper. The focus of this paper is to design and develop the hardware architecture to meet the requirement of such processing. In the proposed architecture, instead of comparing the whole DNA search string at once, the entire comparison process is split into four phases using four-stage pipeline structure, to boost up the speed of processing by exploiting the inherent temporal parallelism in the search process. Moreover, we reduced memory requirement by 96.86% by arranging DNA sequences in an intelligent manner compared to the straight and conventional method of storing DNA sequences using Content Addressable Memory (CAM). This effectively enhances system throughput by searching more number of DNA sequences against a single DNA sequence in traditional design. It further reduces system size, cost and power by replacing CAM using Random Access Memory (RAM). It is observed that, only a fraction (0.39%) of the total memory available in Stage 2 is activated, while 0.0015% of the total memory is activated in Stage 3 and a very low fraction (0.000006%) of the total memory is activated in Stage 4, during the comparison of a DNA sequence in the proposed four-stage pipelined structure. This effectively lowers the system cost, power consumption, the heat dissipation, and space requirement.
[1]
Partha Pratim Pande,et al.
Network-on-Chip Hardware Accelerators for Biological Sequence Alignment
,
2010,
IEEE Transactions on Computers.
[2]
P. Lala,et al.
A CAM ( Content Addressable Memory )-based architecture for molecular sequence matching
,
2011
.
[3]
D. Lipman,et al.
Improved tools for biological sequence comparison.
,
1988,
Proceedings of the National Academy of Sciences of the United States of America.
[4]
Weiguo Liu,et al.
Streaming Algorithms for Biological Sequence Alignment on GPUs
,
2007,
IEEE Transactions on Parallel and Distributed Systems.
[5]
M S Waterman,et al.
Identification of common molecular subsequences.
,
1981,
Journal of molecular biology.
[6]
Bertil Schmidt,et al.
Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW
,
2005,
Bioinform..
[7]
K. Pagiamtzis,et al.
Content-addressable memory (CAM) circuits and architectures: a tutorial and survey
,
2006,
IEEE Journal of Solid-State Circuits.
[8]
S. B. Needleman,et al.
A general method applicable to the search for similarities in the amino acid sequence of two proteins.
,
1970,
Journal of molecular biology.