VLSI Design and Implementation DNA Sequence Alignment for Hardware Based Applications
Keywords:
DNA sequence, Sequence Alignment, Smith waterman algorithm, gotoh, FPGA, D & C principle.Abstract
In this paper we are going to propose a new approach to map the DNA sequences using Smith waterman algorithm with Gotoh algorithm. In general Bio medical applications sequence mapping plays a major role for identifying various issues regarding diseases, mutations etc. can be analyzed and identified. As the mapping process is the most time consuming process here we are going to resolve it by introducing divide and conquer based approach and implement parallelism for mapping the sequences and we can enhance the performance of mapping sequence process. The proposed implementation is suitable for FPGA hardware utilization which is the prime factor of our suggested implementation. The synthesis and simulation of the proposed implementation can be done using CAD tools & MATLAB for extracting the DNA data.
References
- Yupeng Chen, Bertilschmit, Douglas L. Maskel, “Reconfigurable Accelerator for the Word-Matching Stage of BLASTN,” IEEE Transactions on Very Large Scale Integration (VLSI) Systems, vol. 21, no. 4, pp-659-667, April 2013.
- Snort, Ver.2.8, Network Intrusion Detection System, http:// www.snort.org., 2011.
- Clam AntiVirus, Ver.0.95.3. http://www.clamav.net., 2011.
- C.-H. Lin, Y.-T. Tai, and S.-C. Chang, “Optimization of Pattern Matching Algorithm for Memory Based Architecture,” Proc. Third ACM/IEEE Symp. Architecture for Networking and Comm. Systems, pp. 11-16, 2007.
- Deterministic Finite-State Machine, http://en.wikipedia.org/ wiki/Deterministic_finite_state_machine, 2011.
- H. Kim, H. Hong, H.-S. Kim, and S. Kang, “A Memory-Efficient Parallel String Matching for Intrusion Detection Systems,” IEEE Comm. Letters, vol. 13, no. 12, pp. 1004-1006, Dec. 2009.
- Virtex-4 FPGA User Guide, http://www.xilinx.com/support/ documentation/user_guides/ug070.pdf., 2011.
- F. Yu, Z. Chen, Y. Diao, T.V. Lakshman, and R.H. Katz, “Fast and Memory-Efficient Regular Expression Matching for Deep Packet Inspection,” Proc. Second ACM/IEEE Symp. Architecture for Networking and Comm. Systems, pp. 93-102, 2006.
- A.V. Aho and M.J. Corasick, “Efficient String Matching: An Aid to Bibliographic Search,” Comm. ACM, vol. 18, no 6, pp. 333-340, 1975.
- L. Tan and T. Sherwood, “A High Throughput String Matching Architecture for Intrusion Detection and Prevention,” Proc. 32nd IEEE/ACM Int’l Symp. Computer Architecture, pp. 112-122, 2005.
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