Bio-sequence analysis with cradle's 3SoC™ Software scalable system on chip

Proceedings of the ACM Symposium on Applied Computing

Volumn 1, Issue , 2004, Pages 202-206

  Meng, Xiandong ^a   Chaudhary, Vipin ^b  

^a Wayne State University   (United States)

^b WAYNE STATE UNIVERSITY   (United States)

Author keywords

3SoC chip; Digital Signal Processors; Smith Waterman algorithm

Indexed keywords

3SOC CHIP; SEQUENCE COMPARISON ALGORITHMS; SMITH WATERMAN ALGORITHM;

ALGORITHMS; DATABASE SYSTEMS; DIGITAL SIGNAL PROCESSING; DNA SEQUENCES; GENES; MICROPROCESSOR CHIPS; MULTIPROCESSING SYSTEMS;

COMPUTER SOFTWARE;

EID: 2442533043     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (15)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. Basic local alignment search tool. J. Mol. Biol.215, (1990), 403-410
2. Bjornson, R.D., Sherman, A.H., Weston, S.B., Willard, N. and Wing, J. TurboBLAST: A Parallel Implementation of BLAST Built on the TurboHub, International Parallel and Distributed Processing Symposium: IPDPS Workshops (2002), p.0183
3. Eyre, J. and Bier, J DSP Processors Hit the Mainstream. IEEE Computer Magazine (1998) Vol. 31, No. 8. pp. 51-59
4. Gotoh, O. An improved algorithm for matching biological sequences J. Mol.Biol.(1982) 162, 705-708
5. Grate, L., Diekhan, M., Dahle, D. and Hughey, H. Sequence Analysis With the Kestrel SIMD parallel Processor.Pacific Symposium on Biocomputing 2001 pp.263-74
6. Hughey, R. Parallel hardware for sequence comparison and alignment. (1996) Comput. Appl. Biosci. 12, 473-479
7. Lau, F. An Integrated Approach to Fast, Sensitive, and Cost-Effective Smith-Waterman Multiple Sequence Alignment. Bioinformatics Module, (2000) MB&B 452
8. Needleman, S. and Wunsch, C. A general method applicable to the search for similarities in the amino acid sequence of two sequences. . J. Mol. Biol., 48(3), (1970), 443-453
9. Rogens, T. and Seeberg. E. Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors. Bioinformatics, 16, (2000), 699-706.
10. Schmidt, B., Schroder, H. and Schimmler, M. Massively Parallel Solutions for Molecular Sequence Analysis, International Parallel and Distributed Processing Symposium: IPDPS Workshops (2002), p. 0186
11. Smith, T.F. and Waterman, M.S. Identification of common molecular subsequences. J. Mol. Biol., 147, (1981), 195-197
12. Taylor, Stewart Applying MMX Technology to the Smith-Waterman Algorithm. Department of Electrical Engineering, Stanford University, www.stanford.edu/ ~sntaylor/mis299/report.htm
13. Yamagucchi Y., Maruyama, T. High Speed Homology Search with FPGA. Pacific Symposium on Biocomputing 2002
14. 3SoC Documentation - 3SoC 2003 Hardware Architecture, Cradle Technologies, Inc. Mar 2002.
15. 3SoC Programmer's Guide, Cradle Technologies, Inc., http://www.cradle. com, Mar 2002.