Sequence alignment with traceback on reconfigurable hardware

Proceedings - 2008 International Conference on Reconfigurable Computing and FPGAs, ReConFig 2008

Volumn , Issue , 2008, Pages 259-264

  Lloyd, Scott ^a   Snell, Quinn O ^a  

^a Brigham Young University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIO-MEDICAL APPLICATIONS; BIOLOGICAL SEQUENCE ALIGNMENTS; DESKTOP COMPUTERS; FPGA TECHNOLOGIES; GENETIC DATUM; I/O BOTTLENECKS; PERFORMANCE GAINS; PROCESSING ELEMENTS; RECONFIGURABLE HARDWARES; SEQUENCE ALIGNMENTS; SEQUENCE COMPARISONS; SEQUENCE LENGTHS; TRACEBACK;

BIOCHEMISTRY; COMPUTER HARDWARE; DECODING; FIELD PROGRAMMABLE GATE ARRAYS (FPGA); MOLECULAR BIOLOGY;

ALIGNMENT;

EID: 62349112218     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ReConFig.2008.30     Document Type: Conference Paper

References (22)

1. Seq-Gen. http://tree.bio.ed.ac.uk/software/seqgen/.
2. E. W. Edmiston, N. G. Core, J. H. Saltz, and R. M. Smith. Parallel processing of biological sequence comparison algorithms. International Journal of Parallel Programming, 17(3):259-275, 1988.
3. S. N. Gardner, M. W. Lam, N. J. Mulakken, C. L. Torres, J. R. Smith, and T. R. Slezak. Sequencing needs for viral diagnostics. Journal of Clinical Microbiology, 42(12):5472-5476, December 2004.
4. O. Gotoh. An improved algorithm for matching biological sequences. Journal of Molecular Biology, 162(3):705-708, December 1982.
5. X. Guan and E. C. Uberbacher. A multiple divide-and-conquer (MDC) algorithm for optimal alignments in linear space. Technical Report ORNL/TM-12764, Oak Ridge National Lab., June 1994.
6. D. T. Hoang and D. P. Lopresti. FPGA implementation of systolic sequence alignment. In H. Grünbacher and R. W. Hartenstein, editors, Field-Programmable Gate Arrays: Architectures and Tools for Rapid Prototyping, pages 183-191. Springer-Verlag, Berlin, 1992.
7. R. P. Jacobi, M. Ayala-Rincón, L. G. Carvalho, C. H. Llanos, and R. W. Hartenstein. Reconfigurable systems for sequence alignment and for general dynamic programming. Genetics and Molecular Research, 4(3):543-552, September 2005.
8. R. Lipton and D. Lopresti. Comparing long strings on a short systolic array. In W. Moore, A. McCabe, and R. Urquhart, editors, Systolic Arrays, pages 363-376. Hilger, 1987.
9. S. Lloyd and Q. Snell. Qnet: A modular architecture for reconfigurable computing. In Procedings of the 2008 International Conference on Engineering of Reconfigurable Systems and Algorithms (ERSA'08), pages 259-265, July 2008.
10. C. Macken, H. Lu, J. Goodman, and L. Boykin. The value of a database in surveillance and vaccine selection. International Congress Series, 1219:103-106, October 2001.
11. G. L. Moritz, C. Jory, H. S. Lopes, and C. R. E. Lima. Implementation of a parallel algorithm for protein pairwise alignment using reconfigurable computing. In Reconfigurable Computing and FPGA's (ReConFig), pages 99-105. IEEE, September 2006.
12. E. W. Myers and W. Miller. Optimal alignments in linear space. Comput. Appl. Biosci., 4(1):11-17, 1988.
13. S. B. Needleman and C. D. Wunsch. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48(3):443-453, 1970.
14. C. Notredame, D. G. Higgins, and J. Heringa. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, 302(1):205-217, September 2000.
15. PCI-SIG. PCI Express. http://www.pcisig.com/.
16. S. Rajko and S. Aluru. Space and time optimal parallel sequence alignments. IEEE Transactions on Parallel and Distributed Systems, 15(12):1070-1081, December 2004.
17. T. Ramdas and G. Egan. A survey of FPGAs for acceleration of high performance computing and their application to computational molecular biology. In TENCON 2005 IEEE Region 10, pages 1-6, November 2005.
18. C. Sanderson. Simplify FPGA application design with DIMEtalk. Xcell Journal, Winter(51):104-107, 2004.
19. T. F. Smith and M. S. Waterman. Identification of common molecular subsequences. Journal of Molecular Biology, 147(1):195-197, March 1981.
20. J. D. Thompson, D. G. Higgins, and T. J. Gibson. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22):4673-4680, 1994.
21. T. VanCourt and M. C. Herbordt. Families of FPGA-based accelerators for approximate string matching. Microprocessors and Microsystems, 31(2):135-145, March 2007.
22. Y. Yamaguchi, T. Maruyama, and A. Konagaya. High speed homology search with FPGAs. In Pacific Symposium on Biocomputing, pages 271-282, 2002.