Large scale protein sequence alignment using FPGA reprogrammable logic devices

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3203, Issue , 2004, Pages 23-32

  Dydel, Stefan ^a   Bała, Piotr ^a  

^a NICOLAUS COPERNICUS UNIVERSITY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOINFORMATICS; GENERAL PURPOSE COMPUTERS; LOGIC DEVICES; PROTEINS; SEARCH ENGINES; SYSTOLIC ARRAYS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; FPGA-BASED IMPLEMENTATION; LARGE SCALE PROTEINS; ORDERS OF MAGNITUDE; PROTEIN SEQUENCE ALIGNMENTS; REPROGRAMMABLE LOGIC; SMITH-WATERMAN ALGORITHM;

FIELD PROGRAMMABLE GATE ARRAYS (FPGA);

EID: 35048890993     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-30117-2_5     Document Type: Article

References (29)

1. C.W. Yu, K.H. Kwong, K.H. Lee and P.H.W. Leong. A Smith-Waterman Systolic Cell.Proceedings of the Tenth International Workshop on Field Programmable Logic and Applications (FPL'03), Lisbon, pp. 375-384, 2003
2. B. West, R. D. Chamberlain, R. Indeck, and Q. Zhang. An FPGA-based Search Engine for Unstructured Database. Proc. of 2nd Workshop on Application Specific Processors, December 2003.
3. N. Weaver, Y. Markovskiy, Y. Patel, J. Wawrzynek. Post Placement C-slow Retiming for the Xilinx Virtex FPGA. 11th ACM Symposium of Field Programmable Gate Arrays (FPGA) , 2003
4. S. A. Guccione and E. Keller. Gene matching using JBits. Field-Programmable Logic and Applications, Reconfigurable Computing 12th International Conference, p. 1168-1171, September 2-4, 2002.
5. Y. Yamaguchi, T. Maruyama and A. Konagaya. High Speed Homology Search with FPGAs. Pacific Symposium on Biocomputing 7:271-282, 2002.
6. T. Rognes and E. Seeberg. Six-fold speedup of Smith-Waterman sequence database searches using parallel processing on common microprocessors.Bioinformatics, Vol. 16 no. 8, 2000, p. 699-706
7. D. Lavenier. Speeding up genome computations with a systolic accelerator. SIAM News, vol. 31, no. 8, Oct. 1998.
8. J. D. Hirshber, R. Hughey, K. Karplus. Kestrel. A Programmable Array for Sequence Analysis. Proc. Int. Conf. Application-Specific Systems, Architectures, and Processors, IEEE CS, Aug. 19-21, 1996, pp. 25-35
9. D. Lavenier. SAMBA: Systolic Accelerators for Molecular Biological Applications, IRISA Report, (PI-988) , March 1996.
10. D. T. Hoang. Searching genetic databases on splash 2. Proceedings 1993 IEEE Workshop on Field-Programmable Custom Computing Machines, p. 185-192, 1993.
11. Hoang, Dzung T. FPGA Implementation of Systolic Sequence Alignment. International Workshop on Field Programmable Logic and Applications, Vienna, Austria, Aug. 31 - Sept. 2, 1992.
12. R.J. Lipton, and D. Lopresti. A systolic array for rapid string comparison. Proceedings of the Chapel Hill Conference on VLSI, p. 363-376, 1985.
13. Paracel, inc. http://www.paracel.com.
14. Sencel's search software. http://www.sencel.com.
15. Celera genomics, inc. http://www.celera.com.
16. M. Crochemore, C.Iliopoulos, Y. Pinzon, J. Reid. A Fast and Practical Bit-Vector Algorithm for the Longest Common Subsequence Problem. Information Processing Letters, Vol. 80, Issue 6, p. 279 - 285, Dec. 2001
17. T. F. Smith, M. S. Waterman. Identifcation of Common Molecular Subsequences. Journal of Molecular Biology, 147(1):195-197, 1981.
18. M. S. Waterman. Introduction to Computational Biology: Sequences, Maps and Genomes. Chapman and Hall, London, 1995.
19. W. R. Pearson. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11(3):635-650, 1991
20. W. R. Pearson, D. J. Lipman. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85(8), 2444-2448, 1988.
21. W. R. Pearson. Rapid and sensitive sequence comparison with fastp and fasta. Methods in Enzymology, 183:63-98, 1990.
22. B. Ma, J. Tromp, M. Li. PatternHunter: Faster and More Sensitive Homology Search. Bioinformatics. 18(3):440-5, 2002.
23. G. Z. Hertz, G. D. Stormo. Identifing DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15(7/8):563-577, 1999.
24. A. Davidson. A Fast Pruning Algorithm for Optimal Sequence Alignment. Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001). IEEE Comput. Soc. Los Alamitos CA, USA, pp.49-56, 2001.
25. S. Henikoff, J. G. Henikoff. Amino acid substitution matrices from protein blocks. Proc. matl. Acad. Sci. USA. 89, 10915-10919, 1992.
26. Timelogic home page. http://www.timelogic.com
27. Xilinx home page. http://www.xilinx.com
28. Synplicity home page. http://www.synplicity.com
29. Opencores home page. http://www.opencores.org