Acceleration of ungapped extension in Mercury BLAST

Microprocessors and Microsystems

Volumn 33, Issue 4, 2009, Pages 281-289

  Lancaster, Joseph ^a   Buhler, Jeremy ^a   Chamberlain, Roger D ^a,b  

^a WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

^b BECS Technology Inc   (United States)

Author keywords

Biosequence analysis; BLAST; FPGA acceleration; Sequence alignment

Indexed keywords

BIOSEQUENCE ANALYSIS; BIOSEQUENCE COMPARISON; BLAST; BLAST SYSTEMS; CRITICAL SECTIONS; FPGA ACCELERATION; GENERAL PURPOSE PROCESSORS; GENOMIC DATA; PERFORMANCE IMPROVEMENTS; SEQUENCE ALIGNMENT; SOFTWARE TOOL; SPECIALIZED HARDWARE; STANDARD DISTRIBUTIONS; STANDARD SOFTWARE; STREAMING APPROACH;

ALIGNMENT; COMPUTER SOFTWARE; FIELD PROGRAMMABLE GATE ARRAYS (FPGA); GENERAL PURPOSE COMPUTERS; MERCURY (METAL);

RADIO TELESCOPES;

EID: 65649143897     PISSN: 01419331     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.micpro.2009.02.007     Document Type: Article

References (23)

1. National Center for Biological Information, Growth of GenBank, 2002. .
2. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
3. Waterston R.H., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420 (2002) 520-562
4. Altschul S.F., and Gish W. Local alignment statistics. Methods: A Companion to Methods in Enzymology 266 (1996) 460-480
5. Altschul S.F., Gish W., Miller W., Myers E.W., et al. Basic local alignment search tool. Journal of Molecular Biology 215 (1990) 403-410
6. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25 (1997) 3389-3402
7. Paracel, Paracel, Inc., 2006. .
8. Timelogic, TimeLogic Corporation, 2006. .
9. P. Krishnamurthy, J. Buhler, R.D. Chamberlain, M.A. Franklin, K. Gyang, J. Lancaster, Biosequence similarity search on the Mercury system, in: Proceedings of the 15th IEEE International Conference on Application-Specific Systems, Architectures, and Processors, 2004, pp. 365-375.
10. Smith T.F., and Waterman M.S. Identification of common molecular subsequences. Journal of Molecular Biology 147 1 (1981) 195-197
11. R.D. Chamberlain, R.K. Cytron, M.A. Franklin, R.S. Indeck, The mercury system: exploiting truly fast hardware for data search, in: Proceedings of International Workshop on Storage Network Architecture and Parallel I/Os, 2003, pp. 65-72.
12. Zhang Z., Schwartz S., Wagner L., and Miller W. A greedy algorithm for aligning DNA sequences. Journal of Computational Biology 7 (2000) 203-214
13. Ning Z., Cox A.J., and Mullikin J.C. SSAHA: a fast search method for large DNA databases. Genome Research 11 (2001) 1725-1729
14. Kent W.J. BLAT: the BLAST-like alignment tool. Genome Research 12 (2002) 656-664
15. G. Knowles, P. Gardner-Stephen, DASH: localizing dynamic programming for order of magnitude faster, accurate sequence alignment, in: Proceedings of the IEEE Computational Systems Bioinformatics Conference, 2004, pp. 732-735.
16. Li M., Ma B., Kisman D., and Tromp J. Patternhunter II: highly sensitive and fast homology search. Journal of Bioinformatics and Computational Biology 2 (2004) 417-439
17. G. Knowles, P. Gardner-Stephen, A new hardware architecture for genomic and proteomic sequence alignment, in: Proceedings of the IEEE Computational Systems Bioinformatics Conference, 2004, pp. 730-731.
18. R.K. Singh, et al., BioSCAN: a dynamically reconfigurable systolic array for biosequence analysis, in: Proceedings of CERCS'96, 1996.
19. J.D. Hirschberg, R. Hughley, K. Karplus, Kestrel: a programmable array for sequence analysis, in: Proceedings of IEEE International Conference on Application-Specific Systems, Architecture, and Processors, 1996, pp. 23-34.
20. D.T. Hoang, Searching genetic databases on Splash 2, in: IEEE Workshop on FPGAs for Custom Computing Machines, 1995, pp. 185-191.
21. N. Pappas, Searching Biological Sequence Databases Using Distributed Adaptive Computing, Master's Thesis, Virginia Polytechnic Institute and State University, 2003.
22. Y. Yamaguchi, T. Maruyama, A. Konagaya, High speed homology search with FPGAs, in: Pacific Symposium on Biocomputing, 2002, pp. 271-282.
23. D. Lavenier, S. Guytant, S. Derrien, S. Rubin, A reconfigurable parallel disk system for filtering genomic banks, in: Proceedings of International Conference on Engineering of Reconfigurable Systems and Algorithms, 2003, pp. 154-166.