Exploiting coarse-grained parallelism to accelerate protein motif finding with a network processor

Parallel Architectures and Compilation Techniques - Conference Proceedings, PACT

Volumn 2005, Issue , 2005, Pages 173-184

  Wun, Ben ^a   Buhler, Jeremy ^a   Crowley, Patrick ^a  

^a WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHIP MULTIPROCESSOR (CMP); HIDDEN MARKOV MODELS (HMM); MULTI-CORE ARCHITECTURES; VITERBI ALGORITHM;

CHIP SCALE PACKAGES; COMPUTER ARCHITECTURE; COMPUTER NETWORKS; COMPUTER SOFTWARE; COMPUTER WORKSTATIONS; MARKOV PROCESSES; MATHEMATICAL MODELS; PARALLEL PROCESSING SYSTEMS;

MICROPROCESSOR CHIPS;

EID: 33746696604     PISSN: 1089795X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/PACT.2005.21     Document Type: Conference Paper

References (29)

1. Intel Pentium 4 Processor Family Product Information. http://www.intel.com/prodcuts/desktop/processors/pentium 4.
2. HMMER: Sequence Analysis Using Profile Hidden Markov Models. http://hmmer.wustl.edu.2004.
3. Hoel, P.G. Introduction to Mathematical Statistics, 3rd ed. New York: Wiley, 1962, page 57.
4. Alex Bateman, et al. The Pfam Protein Families Database. Nucleic Acids Research(2004) 32:D138-D141.
5. Boeckmann B., et al.: The Swiss-Prot protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:365-370(2003).
6. Austin, T.M., Burger, D. The SimplScalar Tool Set, Version 2.0. http://www.simplescalar.com. 2003.
7. "Pthreads: POSIX threads standard", IEEE Standard 1003.1c-1995.
8. Chandra, P., et al (2003). Intel IXP 2400 Network Processor: A Second-Generation Intel NPU. Crowley, P., et al. (Eds.), Network Processor Design Issues and Practices vol. 1 (pp.259-275). San Fransisco, CA: Morgan Kaufmann Publishers.
9. Marshall, J. (2003). Toaster2. Crowley, P., et al. (Eds.), Network Processor Design Issues and Practices vol. 1 (pp.235-248). San Francisco, CA: Morgan Kaufmann Publishers.
10. Montavista Software- Powering the Embedded Revolution. http://www.mvista.com.
11. Radisys: Embedded Systems and Solutions. http://www.radisys.com.
12. Intel 21555 Non-transparent PCI-toPCI Bridge. http://www.intel.com/design/bridge/21555.htm.
13. Rabiner, L.R. A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77:257-86, 1989.
14. th Annual Hawaii Int'l Conf. on System Sciences, volume 1, 792-802, IEEE Computer Society Press, 1993.
15. Krogh, A. Hidden Markov models for labeled sequences. In Proceedings of the 12th IAPR Int'l Conf. on Pattern Recognition, 140-144, IEEE Computer Society Press, 1994.
16. Graham, S., Kessler, P., and McKusick, M. gprof: A Call Graph Execution Profiler. In Proc. of the SIGPLAN '82 Symp. on Compiler Construction (Boston, MA, June 1982), Association for Computing Machinery, pp. 120-126.
17. Intel C++ Compiler for Linux User's Guide. Intel Corporation, 2003.
18. Free Software Foundation (FSF), GCC Home Page. http://www.gnu.org/sortware/gcc/gcc.html. 2004.
19. J. Vlontzos, S. Kung. "Hidden Markov Models for Character Recognition", IEEE transactions on image processing, 1(4), oct 1992.
20. A. Kundu, Y. He, P. Bahl, "Recognition of handwritten word: first and second order hidden markov model based approach", Pattern recognition, 22(3), 1989
21. K. Aas, L. Eikvil, R.B. Huseby, "Applications of hidden Markov chains in image analysis", Pattern recognition, 32(4), p. 703, 1999.
22. , J. Li, A. Najmi, R.M. Gray, "Image Classification by a Two-Dimensional Hidden Markov Model" IEEE transactions on signal processing, 48(2), p. 517, Feb 2000.
23. T. Ryden, et al, "Stylized Facts of Daily Return Series and the Hidden Markov Model", Journal of applied econometrics, 13(3), p. 217, May 1998.
24. Dirk Outston et al. "Applications of hidden Markov models to detecting multi-stage network attacks." In Proc. of the 36th Hawaii Int'l Conf. on System Sciences, IEEE Computer Society Press, 334-344, 2003.
25. DeCypherHMM Solution. http://www.timelogic.com/decypher_hmm.htm, 2004.
26. Bos, H. and Huang, K. "On the Feasibility of Using Network Proceessor for DNA Queries". In Proc. of the Third Workshop on Network Processors & Applications (NP-3), pp. 183-195, 2004.
27. Intel Vtune Performance Analyzers. www.intel.com/softwaro/products/vtune/
28. Chukkapalli G., Guda, C. and Subramaniam S. SledgeHMMER: A web server for batch searching Pfam database, Nucleic Acids Res., 32:W542-544
29. HMMERHEAD, Unpublished; http://www.cs.huji.ac.il/labs/compbio/hmmerhead/