Methodology for evaluating DNA pattern searching algorithms on multiprocessor

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

Volumn , Issue , 2007, Pages 570-577

  Soewito, Benfano ^a   Weng, Ning ^a  

^a Southern Illinois University Carbondale   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; DNA; GENES; LEARNING ALGORITHMS; NUCLEIC ACIDS; ORGANIC ACIDS; PATTERN MATCHING;

ANALYTICAL PERFORMANCE MODELS; AUTOMATIC SIMULATIONS; CASE STUDIES; DNA PATTERNS; EVALUATION METHODOLOGIES; MATCHING ALGORITHMS; MULTI-PROCESSORS; MULTICORE; MULTICORE PROCESSORS; PATTERN SEARCH ALGORITHMS; PRIOR WORKS; STRING MATCHING ALGORITHMS; SYSTEM'S PERFORMANCES; TASK GRAPHS; UNIPROCESSOR;

MULTIPROCESSING SYSTEMS;

EID: 47649116551     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2007.4375618     Document Type: Conference Paper

References (25)

1. S. Wu and U. Manber, "Agrep - a fast approximate pattern-matching tool," in Proceedings USENIX Winter 1992 Technical Conference, San Francisco, CA, 1992, pp. 153-162.
2. The Open Source Network Instrusion Detection System, Snort, Inc., 2004, http://www.snort.org.
3. M. Miyazaki, S. Fukamachi, M. Takeda, and T. Shinohara, "Speeding up the pattern matching machine for compressed texts," Transactions of Information Processing, vol. 39, pp. 2638-2648, 1998.
4. A. Aho and M. Corasick, "Efficient string matching: An aid to bibliographic search," Communications of the ACM, vol. 18, 1975.
5. S. Wu and Manber, "A fast algorithm for multi-pattern searching," Department of Computer Science, University of Arizona, Tech. Rep. TR94-17, 1994.
6. DNA Sequence Database, Natinal Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/.
7. R. Ramaswamy and T. Wolf, "PacketBench: A tool for workload characterization of network processing," in Proc. of IEEE 6th Annual Workshop on Workload Characterization (WWC-6), Austin, TX, Oct. 2003, pp. 42-50.
8. N. Weng and T. Wolf, "Profiling and mapping of parallel workloads on network processors," in Proc. of The 20th Annual ACM Symposium on Applied Computing (SAC), Santa Fe, NM, Mar. 2005, pp. 890-896.
9. N. Weng and T. Wolf., "Pipelining vs. multiprocessors - choosing the right network processor system topology," in Proc. of Advanced Networking and Communications Hardware Workshop (ANCHOR 2004) in conjunction with The 31st Annual International Symposium on Computer Architecture (ISCA 2004), Munich, Germany, June 2004.
10. D. Denning, "An intrusion-detection model," IEEE Transactions on Software Engineering, vol. 13, no. 2, pp. 222-232, Feb. 1987.
11. Y. Lu, S. Lu, and J. L. Ram, "Fast search in dna sequence databases using punctuation and indexing," in ACST'06: Proceedings of the 2nd IASTED international conference on Advances in computer science and technology. Anaheim, CA, USA: ACTA Press, 2006, pp. 351-356.
12. R. S. Boyer and J. S. Moore, "A fast string searching algorithm," Communication of the ACM, vol. 20, no. 10, pp. 762-772, 1977.
13. B. Commentz-Walter, "A string matching algorithm fast on the average," in Proc. of the 6th International Colloquium on Automata, Languages and Programming, vol. 71, 1979.
14. L. Chen, S. Lu, and J. Ram, "Compressed pattern matching in dna sequences," in CSB '04: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (CSB'04). Washington, DC, USA: IEEE Computer Society, 2004, pp. 62-68.
15. N. Tuck, T. Sherwood, B. Calder, and G. Varghese, "Deterministic memory-efficient string matching algorithms for intrusion detection." in Proc. of the IEEE Infocom Conference, 2004.
16. E. P. Markatos, S. Antonatos, M. Polychronakis, and K. G. Anagnostakis, "Exclusion-based signature matching for intrusion detection," in Proc. of the IASTED International Conference on Communication and Computer Networks, Nov. 2002, pp. 146-152.
17. S. Dharmapurikar, P. Krishnamurthy, T. Sproull, and J. Lockwood, "Deep packet inspection using parallel bloom filters," IEEE Micro, vol. 24, no. 1, pp. 52-61, Jan. 2004.
18. E. S. de Moura, G. Navarro, N. Ziviani, and R. A. Baeza-Yates, "Direct pattern matching on compressed text," in String Processing and Information Retrieval, 1998, pp. 90-95.
19. G. Navarro and J. Tarhio, "Lzgrep: a boyer moore string matching tool for ziv lempel compressed text: Research articles," Softw. Pract. Exper., vol. 35, no. 12, pp. 1107-1130, 2005.
20. J. Hrisson, G. Payen, and R. Gherbi, "A 3d pattern matching algorithm for dna sequences," Bioinformatics, vol. 23, no. 6, pp. 680-686, 2007.
21. Z. K. Baker and V. K. Prasanna, "Time and area efficient pattern matching on fpgas," in FPGA '04: Proceedings of the 2004 ACM/SIGDA 12th international symposium on Field programmable gate arrays. New York, NY, USA: ACM Press, 2004, pp. 223-232.
22. H. Song and J. W. Lockwood, "Efficient packet classification for network intrusion detection using fpga," in FPGA '05: Proceedings of the 2005 ACM/SIGDA 13th international symposium on Field-programmable gate arrays. New York, NY, USA: ACM Press, 2005, pp. 238-245.
23. Y. Sugawara, M. Inaba, , and K. Hiraki, "Over 10gbps string matching mechanism for multi-stream packet scanning systems," in Lecture Notes in Computer Science, vol. 3203. Springer-Verlag, 2004, pp. 484-493.
24. F. Yu, R. H. Katz, and T. V. Lakshman, "Gigabit rate packet pattern-matching using team," in ICNP '04: Proceedings of the Network Protocols, 12th IEEE International Conference on (ICNP'04). Washington, DC, USA: IEEE Computer Society, 2004, pp. 174-183.
25. S. Dharmapurikar, P. Krishnamurthy, T. S. Sproull, and J. W. Lockwood, "Deep packet inspection using parallel Bloom filters," IEEE Micro, vol. 24, no. 1, pp. 52-61, Jan. 2004.