Aligning biological sequences on distributed bus networks: A divisible load scheduling approach

IEEE Transactions on Information Technology in Biomedicine

Volumn 9, Issue 4, 2005, Pages 489-501

  Min, Wong Han ^a   Veeravalli, Bharadwaj ^b  

^a AGENCY FOR SCIENCE   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Biological sequences; Communication time; Divisible load theory(DLT); Sequence alignment; Smith Waterman algorithm

Indexed keywords

ALGORITHMS; COMPUTATIONAL METHODS; DNA SEQUENCES; HEURISTIC METHODS;

BIOLOGICAL SEQUENCES; DIVISIBLE LOAD THEORY (DLT); SEQUENCE ALIGNMENT; SMITH-WATERMAN ALGORITHM;

MULTIPROCESSING SYSTEMS;

DNA;

ALGORITHM; ANIMAL; ARTICLE; CHEMISTRY; COMPUTER ANALYSIS; COMPUTER NETWORK; GENETICS; METHODOLOGY; MOUSE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SIGNAL PROCESSING;

ALGORITHMS; ANIMALS; COMPUTER COMMUNICATION NETWORKS; COMPUTING METHODOLOGIES; DNA; MICE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SIGNAL PROCESSING, COMPUTER-ASSISTED;

EID: 29444435065     PISSN: 10897771     EISSN: None     Source Type: Journal    
DOI: 10.1109/TITB.2005.855559     Document Type: Article

References (28)

1. GenBank [Online]. Available: http://www.ncbi.nlm.nih.gov
2. M. Gribskov and D. John, Sequence analysis primer, University of Wisconsin Biotechnology Center (UWBC) Biotech Resource Series, Oxford, U.K., Oxford Univ. Press, 1991, [Ontine]. Available: http://www.oup.com/ us/catalog/general/subject/Lifesciences/Molecular-CellBiology/ Biotechnology/?view=usa&ci=0195098749
3. M. S. Waterman, Mathematical Methods for DNA Sequences. Boca Raton, FL: CRC Inc., 1986.
4. T. K. Yap, F. Ophir, and L. Robert, "Parallel computation in biological sequence analysis," IEEE Trans. Parallel Distrib. Syst., vol. 9, p. 3, Mar. 1998.
5. S. B. Needleman and C. D. Wunsch, "A general method applicable to the search for similarities in the amino acid sequence of two sequences," J. Mol. Biology, vol. 48, pp. 443-453, 1970.
6. P. H. Sellers, "On the theory and computation of evolutionary distances," SIAM J. Appl. Math., vol. 26, pp. 787-793, 1974.
7. M. S. Waterman, T. F. Smith, and W. A. Beyer, "Some biological sequence metrics," Advances in Mathematics, vol. 20, pp. 367-387, 1976.
8. T. F. Smith and M. S. Waterman, "Identification of common molecular subsequence," J. Mol. Biology, pp. 195-197, 1981.
9. The EMBL (european molecular biology laboratory) nucleotide sequence database [Online]. Avallable: http://www.ebi.ac.uk/embl
10. O. Gotoh, "An improved algorithm for matching biological sequences," J. Mol. Biology, vol. 162, pp. 705-708, 1982.
11. DNA data bank of japan [Online]. Available: http://www.ddbj.nig.ac.jp
12. D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, B. A. Rapp, and D. L. Wheeler, "GenBank," Nucleic Acids Research, vol. 28, no. 1, pp. 15-18, 2000.
13. E. W. Myers, "An O(ND) difference algorithm and its variations," Algorithmica, vol. 1, no. 2, pp. 251-266, 1986.
14. T. K. Yap, O. Frieder, and R. L. Martino, High performance computational methods for biological sequence analysis. Norwell, MA: Kluwer, 1996.
15. O. Trelles, M. A. Andrade, A. Valencia, E. L. Zapata, and J. M. Carazo, "Computational space reduction and parallelization of a new clustering approach for large groups of sequences," Bioinformatics, vol. 14, no. 5, pp. 439-451, Jun. 1998.
16. T. Rognes and S. Erling, "Six-fold speedup of smith-waterman sequence database seaches using parallel processing on common microprocessors," Bioinformatics, vol. 16, no. 8, pp. 699-706, 2000.
17. M. P. Berger and P. J. Munson, "A novel randomized iteration strategy for aligning multiple protein sequences," Computer Applications in the Bioscience, vol. 7, pp. 479-484, 1991.
18. V. Bharadwaj, D. Ghose, V. Mani, and T. G. Robertazzi, Scheduling Divisible Loads in Parallel and Distributed Systems. Los Alamitos, CA: IEEE Computer Soc. Press, 1996.
19. V. Bharadwaj, D. Ghose, and T. G. Robertazzi, "Divisible load theory: A new paradigm for load scheduling in distributed systems," Cluster Comput. (Special Issue on Divisible Load Scheduling) vol. 6, no. 1, Jan. 2003.
20. T. G. Robertazzi, Scheduling in Parallel and Distributed Systems. [Online]. Available: http://www.ee.sunysb.edu/~tom/dlt.html.
21. V. Bharadwaj and G. Barlas, "Access time minimization for distributed multimedia applications," Multimedia Tools and Applications, vol. 12, no. 2-3, Nov. 2000.
22. X. Li, B. Veeravalli, and C. C. Ko, "Distributed image processing on a network of workstations," Int. J. Comput. Appl., ACTA Press, vol. 25, no. 2, 2003.
23. M. Drozdowski and P. Wolniewicz, "Experiments with scheduling divisible tasks in clusters of workstations," in Euro-Par 2000. LNCS 1900, New York: Springer-Verlag, 2000, pp. 311-319.
24. S.K. Chan, V. Bharadwaj, and D. Ghose, "Large matrix-vector products on distributed bus networks with communication delays using the divisible load paradigm: Performance analysis and simulation," Math. Comput. Simul., vol. 58, pp. 71-79, 2001
25. E. W. Myers and W. Miller, "Optimal alignments in linear space," Comput. Appl. Biosciences, vol. 4, pp. 11-17, 1988.
26. M. Dayhoff, R. M. Schwartz, and B. C. Orcutt, "A model of evolutionary change in proteins," Atlas of Protien Sequences and Structure, National Biomedical Research Foundation, Washington, DC, vol. 5, pp. 345-352, 1978.
27. V. Bharadwaj and N. Viswanadham, "Sub-optimal solutions using integer approximation techniques for scheduling divisible loads on distributed bus networks," IEEE Trans. Syst., Man, and Cybern. A, Syst., Humans, vol. 30, no. 6, pp. 680-691, Nov. 2000.
28. P. Green, SWAT [Online]. Available: http://www.genome.washington.edu/ UWGC/analysistools/Swat.cfm