Parallel pattern identification in biological sequences on clusters

IEEE Transactions on Nanobioscience

Volumn 2, Issue 1, 2003, Pages 29-34

  Huang, Chun Hsi ^a   Rajasekaran, Sanguthevar ^a  

^a University of Connecticut   (United States)

Author keywords

Cluster computing; Parallel algorithm; Tandem repeats

Indexed keywords

ALGORITHMS; COMPUTATIONAL METHODS; COST EFFECTIVENESS; DATABASE SYSTEMS; DISEASES; DISTRIBUTED COMPUTER SYSTEMS; DNA; GENES; NEUROLOGY; SYNCHRONIZATION; VLSI CIRCUITS;

BIOLOGICAL SEQUENCES; CLUSTER COMPUTING; TANDEM REPEATS;

PATTERN RECOGNITION;

EUKARYOTA; PROKARYOTA;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER ANALYSIS; COMPUTER NETWORK; DNA SEQUENCE; EVALUATION; GENE EXPRESSION PROFILING; GENETICS; METHODOLOGY; SEQUENCE ALIGNMENT; TANDEM REPEAT; VALIDATION STUDY;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTER COMMUNICATION NETWORKS; COMPUTING METHODOLOGIES; GENE EXPRESSION PROFILING; PATTERN RECOGNITION, AUTOMATED; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TANDEM REPEAT SEQUENCES;

EID: 3042742809     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2003.810165     Document Type: Article

References (15)

1. G. Benson, "Tandem Repeats Finder - A Program to Analyze DNA Sequences," Nucleic Acids Res., vol. 27, pp. 573-580, 1999.
2. O. Berkman, B. Schieber, and U. Vishkin, "Optimal doubly logarithmic parallel algorithms based on finding all nearest smaller values," J. Algorithms, vol. 14, pp. 344-370, 1993.
3. D. Breslauer and Z. Galil, "An Optimal O(log log n) Time Parallel String Matching algorithm," SIAM J. Comput., vol. 19, pp. 1050-1058, 1990.
4. F. Dehne, A. Fabri, and A. Rau-Chaplin, "Scalable parallel geometric algorithms for coarse grained multicomputers," in Proc. 9th ACM Annual Computational Geometry, 1993, pp. 298-307.
5. M. J. Foster and H. T. Kung, "The design of special-purpose VLSI chips," IEEE Computer, vol. 13, pp. 26-40, Jan. 1980.
6. X. He and C.-H. Huang, "Communication efficient BSP Algorithm for all nearest smaller values problem," J. Parallel Distrib. Comput., vol. 61, pp. 1425-1438, 2001.
7. M. Hirata, H. Yamada, H. Nagai, and K. Takahashi, "A versatile data string-search VLSI," IEEE Solid-State Circuits, vol. 23, pp. 329-335, Apr. 1988.
8. J. JáJá, An Introduction to Parallel Algorithms. Reading, MA: Addison-Wesley, 1992.
9. G. M. Landau, E. W. Myers, and J. P. Schmidt, "Incremental string comparison," SIAM J. Comput., vol. 27, pp. 557-582, 1998.
10. G. M. Landau, J. P. Schmidt, and D. Sokol, "An algorithm for approximate tandem repeats," J. Comput. Biol., vol. 8, pp. 1-18, 2001.
11. W. F. McColl, "Scalable computing," in Lecture Notes in Computer Science, Computer Science Today: Recent Trends and Developments, J. van Leeuwen, Ed. Heidelberg, Germany: Springer-Verlag, 1995, vol. 1000, pp. 46-61.
12. J. S. Sim, K. Park, C. S. Iliopoulos, and W. F. Smyth, "Approximate periods of strings," in Lecture Notes in Computer Science, Combinatorial Pattern Matching. Heidelberg, Germany: Springler-Verlag, 1999, pp. 123-133.
13. Y. Takefuji, T. Tanaka, and K. C. Lee, "A parallel string search algorithm," IEEE Trans. Syst., Man, Cybern., vol. 22, pp. 332-336, Mar./Apr. 1992.
14. L. G. Valiant, "A bridging model for parallel computation," Commun. ACM, vol. 33, no. 8, pp. 103-111, 1990.
15. U. Vishkin, "Optimal parallel pattern matching in strings," Inf. Control, vol. 67, pp. 91-113, 1985.