Boosting data throughput for sequence database similarity searches on FPGAs using an adaptive buffering scheme

Parallel Computing

Volumn 35, Issue 1, 2009, Pages 1-11

  Meng, X ^a   Chaudhary, V ^b  

^a TEXAS A AND M UNIVERSITY   (United States)

^b State University of New York   (United States)

Author keywords

Data prefetching; Direct memory access; FPGA; PCI; Smith Waterman algorithm

Indexed keywords

ADAPTIVE ALGORITHMS; COMPUTER PERIPHERAL EQUIPMENT; DATA STORAGE EQUIPMENT; DATABASE SYSTEMS; DNA SEQUENCES; GENERAL PURPOSE COMPUTERS; INTERFACES (COMPUTER); MULTIPROCESSING SYSTEMS; NUCLEIC ACIDS; ORGANIC ACIDS;

DATA PREFETCHING; DIRECT MEMORY ACCESS; FPGA; PCI; SMITH-WATERMAN ALGORITHM;

FIELD PROGRAMMABLE GATE ARRAYS (FPGA);

EID: 58149268840     PISSN: 01678191     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.parco.2008.09.010     Document Type: Article

References (26)

1. Alpha-Data. .
2. Baer J., and Chen T. An evaluation of hardware and software data prefetching. Supercomputing (1991) 176-186
3. Bias D., et al. The kestrel parallel processor. IEEE Transactions on Parallel and Distributed Systems 16 1 (2005) 80-92
4. Chen T.-F., and Baer J.L. A performance study of software and hardware data prefetching schemes. IEEE Transactions on Computers 44 5 (1995) 609-623
5. Cray Inc. .
6. Dydel S., and Bala P. Large scale protein sequence alignment using FPGA reprogrammable logic devices. LNCS 3203 (2004) 23-32
7. D.T. Hoang, Searching genetic databases on Splash 2, in: IEEE Workshop on FPGAs for Custom Computing Machines, IEEE Computer Society Press, 1993, pp. 185-191.
8. Gornish E.H., and Veidenbaum A. An integrated hardware/software data prefetching scheme for shared-memory multiprocessors. International Journal of Parallel Programming 27 1 (1999) 35-70
9. Gotoh O. An improved algorithm for matching biological sequences. Journal of Molecular Biology 162 (1982) 705-708
10. Guccione S.A., and Keller E. Gene matching using JBits, field-programmable logic and applications. LNCS 2438 (2002) 1168-1171
11. Guerdoux-Jamet P., and Lavenier D. SAMBA: Hardware Accelerator for Biological Sequence Comparison CABIOS vol. 13 (1997), Oxford University Press, Oxford pp. 609-615
12. Hughey R. Parallel hardware for sequence comparison and alignment. Computer Applications in the Biosciences 12 (1996) 473-479
13. Kleiman S., Shah D., and Smaalders B. Programming with Threads. first ed. (1996), Prentice Hall
14. X. Meng, V. Chaudhary, Bio-Sequence Analysis with Cradle's 3SoC Software Scalable System on Chip, in: Proceedings of the ACM Symposium on Applied Computing, 2004, pp. 202-206.
15. Meng X., and Chaudhary V. Optimized fine and coarse parallelism for sequence homology search. International Journal of Bioinformatics Research and Applications 2 4 (2006) 44-430
16. Meng X., and Chaudhary V. An adaptive data prefetching scheme for biosequence database search on reconfigurable platforms. Proceedings of the ACM Symposium on Applied Computing (2007) 140-141
17. Oliver T., Schmidt B., and Maskell D. Hyper customized processors for bio-sequence database scanning on FPGAs. IEEE Transactions on Circuits and Systems II 52 12 (2005) 851-855
18. Oliver T.F., Schmidt B., Jakop Y., and Masskell D.L. Accelerating the Viterbi algorithm for profile hidden markov models using reconfigurable hardware. LNCS 3991 (2006) 522-529
19. Rognes T., and Seeberg E. Six-fold speedup of Smith-Waterman sequence database searches using parallel processing on common microprocessors. Bioinformatics 16 8 (2000) 699-706
20. Paracel. .
21. Progeniq Pte. Ltd. .
22. B. Schmidt, H. Schroder, M. Schimmler, Massively parallel solutions for molecular sequence analysis, in: International Parallel and Distributed Processing Symposium: IPDPS'02 (HiComB'02), Ft Lauderdale, FL, IEEE, 2002, pp. 186-193.
23. Smith T.F., and Waterman M.S. Identification of common molecular subsequences. Journal of Molecular Biology 147 (1981) 195-197
24. Starbridge Systems Inc. .
25. Yamagucchi Y., Maruyama T., and Konagaya A. High speed homology search using run-time reconfiguration. LNCS 3438 (2002) 281-291
26. Yu C.W., Kwong K.H., Lee K.H., and Leong P.H.W. A Smith-Waterman systolic cell. LNCS 2778 (2003) 375-384