A hardware accelerator for the fast retrieval of DIALIGN biological sequence alignments in linear space

IEEE Transactions on Computers

Volumn 59, Issue 6, 2010, Pages 808-821

  Boukerche, Azzedine ^a   Correa, Jan M ^b   Melo, Alba Cristina Magalhaes ^a,b   Jacobi, Ricardo P ^b  

^a UNIVERSITY OF OTTAWA   (Canada)

^b UNIVERSITY OF BRASILIA   (Brazil)

Author keywords

Biology and genetics; Dynamic programming; Special purpose and application based systems

Indexed keywords

BIOLOGICAL SEQUENCE ALIGNMENT; BIOLOGICAL SEQUENCES; BIOLOGY AND GENETICS; EXACT ALGORITHMS; FPGA-BASED ARCHITECTURES; GENOMICS; HARDWARE ACCELERATORS; LINEAR SPACES; ORIGINAL ALGORITHMS; SPACE AND TIME;

ACCELERATION; ALGORITHMS; ALIGNMENT; BIOINFORMATICS; BIOLOGY; CHROMOSOMES; DYNAMIC PROGRAMMING; OPTIMIZATION;

COMPUTER SYSTEMS PROGRAMMING;

EID: 77951701991     PISSN: 00189340     EISSN: None     Source Type: Journal    
DOI: 10.1109/TC.2010.42     Document Type: Article

References (35)

1. C. Wang, B. B. Zhou, and A. Zomaya, "Scaling up Genome Similarity Search Services through Content Distribution, " Proc. Int'l Conf. Parallel Processing (ICPP), 2007.
2. R. Durbin, S. Eddy, A. Krogh, and G. Mitchson, Biological Sequence Analysis. Cambridge Univ. Press, 1998.
3. T. F. Smith and M. S. Waterman, "Identification of Common Molecular Subsequences, " J. Molecular Biology, vol. 147, no. 1, pp. 195-197, Mar. 1981.
4. B. Morgenstern, K. Frech, A. Dress, and T. Werner, "DIALIGN: Finding Local Similarities by Multiple Sequence Alignment, " Bioinformatics, vol. 14, no. 3, pp. 290-294, Mar. 1998. (Pubitemid 28395866)
5. R. Siddhartan, "Sigma: Multiple Alignment of Weakly-Conserved Non-Coding DNA Sequence, " BMC Bioinformatics, vol. 7, no. 143, Mar. 2006.
6. M. Schmollinger, K. Nieselt, M. Kaufman, and B. Morgenstern, "DIALIGN P: Fast Pair-Wise and Multiple Sequence Alignment using Parallel Processors, " BMC Bioinformatics, vol. 5, no. 128, Sept. 2004. (Pubitemid 40195378)
7. B. Morgenstern, "DIALIGN: Multiple DNA and Protein Sequence Alignment at BiBiServ, " Nucleic Acids Research, vol. 32, pp. W33-W36, Mar. 2004. (Pubitemid 38997294)
8. T. El-Ghazawi, E. El-Araby, M. Huang, K. Gaj, V. Kindratenko, and D. Buell, "The Promise of High-Performance Reconfigurable Computing, " Computer, vol. 41, no. 2, pp. 69-76, Feb. 2008.
9. IEEE Std 1666-2005, IEEE Standard SystemC Language. IEEE Press, 2006.
10. Forte Design Systems, "Cynthesizer User's Guide For Cynthesizer 2.4.0, " 2005.
11. Altera Corporation, "Introduction to the Quartus II Software Version 8.0, " Technical Manual, www.altera.com/literature/manual/intro-to- quartus2.pdf.
12. S. Needleman and C. Wunsh, "A General Method Applicable to the Search of Similarities in the Amino Acid Sequence of Two Proteins, " J. Molecular Biology, vol. 48, pp. 443-453, 1970.
13. D. Mount, Bioinformatics: Sequence and Genome Analysis. C. S. Harbor Lab Press, 2004.
14. O. Gotoh, "Am Improved Algorithm for Matching Biological Sequences, " J. Molecular Biology, vol. 162, pp. 705-708, 1982.
15. E. W. Myers and W. Miller, "Optimal Alignments in Linear Space, " Computer Applications in the Biosciences (CABIOS), vol. 4, no. 1, pp. 11-17, 1988. (Pubitemid 18072011)
16. D. S. Hirshberg, "A Linear Space Algorithm for Computing Maximal Common Subsequences, " Comm. ACM, vol. 18, pp. 341-343, 1975.
17. H. T. Kung, "Why Systolic Architectures?, " Computer, vol. 15, no. 1, pp. 37-46, Jan. 1982.
18. R. J. Lipton and D. Lopresti, "A Systolic Array for Rapid String Comparison, " Proc. Chapel Hill Conf. VLSI, pp. 363-376, 1985. (Pubitemid 16515932)
19. D. Lavenier, "Speeding up Genome Computations with a Systolic Accelerator, " SIAM News, vol. 31, no. 8, pp. 6-7, 1998.
20. Y. Yamaguchi, T. Maruyama, and A. Konagaya, "High Speed Homology Search with FPGAs, " Proc. Pacific Symp. Biocomputing (PSB), 2002.
21. K. Puttegowda, W. Worek, N. Pappas, A. Dandapani, and P. Athanas, "A Run-Time Reconfigurable System for Gene-Sequence Searching, " Proc. Int'l Conf. VLSI Design, pp. 561-566, 2003.
22. A. Marongiu, P. Palazzari, and V. Rosato, "A Specialized Hardware Device for the Protein Similarity Search, " Concurrency and Computation: Practice and Experience, vol. 16, pp. 917-931, 2004.
23. T. F. Oliver, B. Schmidt, and D. L. Maskell, "Hyper Customized Processors for Bio-Sequence Database Scanning on FPGAs, " Proc. ACM/SIDA Int'l Conf. Field Programmable Gate Arrays, pp. 229-237, 2005. (Pubitemid 40787612)
24. A. Di Bias et al., "The UCSC Kestrel Parallel Processor, " IEEE Trans. Parallel and Distributed Systems, vol. 16, no. 1, pp. 80-92, Jan. 2005.
25. P. Zhang, G. Tan, and G. R. Gao, "Implementation of the Smith-Waterman Algorithm on a Reconfigurable Supercomputing Platform, " Proc. Int'l Conf. High Performance Networking and Computing, pp. 39-48, 2007.
26. X. Jiang, X. Liu, L. Xu, P. Zhang, and N. Sun, "A Reconfigurable Accelerator for Smith-Waterman Algorithm, " IEEE Trans. Circuits and Systems II, vol. 54, no. 12, pp. 1077-1081, Dec. 2007.
27. O. Storaasli, W. Yu, D. Strensky, and J. Maltby, "Performance of FPGA-Based Biological Applications, " Proc. Cray User Group Meeting, May 2007.
28. D. J. Lipman and W. R. Pearson, "Rapid and Sensitive Protein Similarity Searches, " Science, vol. 227, pp. 1435-1441, 1985.
29. M. Abouellail, E. El-Araby, M. Taher, T. El-Ghazawi, and G. B. Newby, "DNA and Protein Sequence Alignment with High Performance Reconfigurable Systems, " Proc. NASA/ESA Conf. Adaptive Hardware and Systems, 2007.
30. B. Harris, A. C. Jacob, J. M. Lancaster, J. Buhler, and T. D. Chamberlain, "A Banded Smith-Waterman FPGA Accelerator for Mercury BlastP, " Proc. Int'l Conf. Field Programmable Logic and Applications, pp. 765-769, 2007.
31. Silicon Graphics Inc., "SGI Reconfigurable Application Specific Computing: Accelerating Production Workflows, " White paper, www.sgi.com/pdfs/3721.pdf., 2006.
32. S. Y. Kung et al., "Wavefront Array Processors-Concept to Implementation, " Computer, vol. 20, no. 7, pp. 18-33, July 1987.
33. J. Lee, V. Narayanan, M. J. Irwin, and W. Wolf, "An Efficient Architecture for Motion Estimation and Compensation in the Transform Domain, " IEEE Trans. Circuits and Systems for Video Technology, vol. 16, no. 2, pp. 191-201, Feb. 2006. (Pubitemid 43269779)
34. D. L. Hung, H. Cheng, and S. Sengkhamyong, "Design of a Hardware Accelerator for Real-Time Moment Compensation: A Wavefront Array Approach, " IEEE Trans. Industrial Electronics, vol. 46, no. 1, pp. 207-218, Feb. 1999.
35. O. B. Efremides, M. P. Bekakos, and D. J. Evans, "Implementation of the Generalized WZ Factorization on a Wavefront Array Processor, " Int'l J. Computer Math., vol. 79, no. 7, pp. 807-815, 2002.