RC-BLAST: Towards a portable, cost-effective open source hardware implementation

Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005

Volumn 2005, Issue , 2005, Pages

  Muriki, Krishna ^a   Underwood, Keith D ^b   Sass, Ron ^c  

^a CLEMSON UNIVERSITY   (United States)

^b SANDIA NATIONAL LABORATORIES   (United States)

^c UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BASIC LOCAL ALIGNMENT SEARCH TOOL (BLAST); MOLECULAR BIOLOGISTS; OPEN SOURCE HARDWARE; RECONFIGURABLE COMPUTING;

ALGORITHMS; DATABASE SYSTEMS; FIELD PROGRAMMABLE GATE ARRAYS; OPEN SYSTEMS; SEARCH ENGINES; WEARABLE COMPUTERS;

COMPUTER HARDWARE;

EID: 33746291611     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPS.2005.373     Document Type: Conference Paper

References (16)

1. S. Altschul, W. Gish, W. Miller, E. W. Myers, and D. Lipman. A basic local alignment search tool. In J.Mol.Biol.215,3,403-310., 1990.
2. P. A.Marongiu and V.Rosato. Prosidis: a special purpose processor for protein similarity discovery. In Proceedings of the Third IEEE International. Workshop on High Performance Computational Biology, April 2003.
3. R. D. Bjornson, A.H.Sherman, S.B.Weston, N. Willard, and J.Wing. Turboblast: A parallel implementation of blast built on the turbohub. In Proceedings of the Third IEEE International Workshop on High Performance Computational Biology, April 2003.
4. U. Food and D. Administration. Parkinson's Disease New Treatments Slow Onslaught of Symptoms. url:http://www.fda.gov/fdac/features/1998/498_pd.html.
5. D. Gusfield. Algorithms on strings, Trees and Sequences. 1997.
6. D. J. Lipman and W. R. Pearson. rapid and sensitive protein similarity searches. In Science 227,4693,1435-1441, 1985.
7. B. S. Manfred Schimmler and H. Schroder. Massively parallel solutions for molecular sequence analysis. In Proceedings of the Third IEEE International Workshop on High Performance Computational Biology, April 2003.
8. K. Muriki. Design and implementation of open source fpga-based accelerator for blast. Master's thesis, Clemson University, Dec. 2004.
9. NCBI. Blast software. Source may be downloaded from http://www.ncbi.nih.gov/BLAST and databases from ftp://ftp.ncbi.nih.gov/blast/db/.
10. D. of Energy. Medical Sciences Division Research Programs. url:http://www.sc.doe.gov/production/ober/msd_res_topic.html.
11. N. I. of Health. Selected Research awards of NIH. url:http://www.nih.gov/about/researchadvances.htm.
12. W. R. Pearson and D. J. Lipman. Improved tools for biological sequence comparison. In Proc.Natl.Acad.Sci. USA 85,8,2444-2448., 1988.
13. H. Simmler, H. Singpiel, and R. Manner. Real time primer design for dna chips. In Proceedings of the Third IEEE International Workshop on High Performance Computational Biology, April 2003.
14. T. F. Smith and M. S. Waterman. Identification of common molecular subsequences. In J.Mol.Biol. 147,1,195-197, 1981.
15. D. Time Logic. Recent Product Citations. url:http://www.timelogic.com/decypher_citations.html.
16. H. Wang, T. H. Ong, B. C. Ooi, and K. L. Tan. Blast++: A tool for blasting queries in batches. In Proceedings of the Third IEEE International Workshop on High Performance Computational Biology, April 2003.