A performance evaluation of a local DNA sequence alignment algorithm on a cluster of workstations

Proceedings - International Parallel and Distributed Processing Symposium, IPDPS 2004 (Abstracts and CD-ROM)

Volumn 18, Issue , 2004, Pages 2327-2334

  Boukerche, Azzedine ^a   De Melo, Alba Cristina Magalhaes Alves ^b   Walter, Maria Emilia Telles ^b   Melo, Renata Cristina Faray ^b   Santana, Marcelo Nardelli Pinto ^b   Batista, Rodolfo Bezerra ^b  

^a UNIVERSITY OF OTTAWA   (Canada)

^b UNIVERSITY OF BRASILIA   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTATIONAL METHODS; COMPUTER WORKSTATIONS; DYNAMIC PROGRAMMING; PROBLEM SOLVING; SYNCHRONIZATION;

OPTIMAL ALIGNMENTS; PARALLEL STRATEGY; SEQUENCE ALIGNMENT; SEQUENCES;

DNA;

EID: 12444269001     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (19)

1. S. F. Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, v. 25, n. 17, p. 3389-3402, 1997.
2. I. Foster, Designing and Building Parallel Programs, Addison-Wesley, 1995.
3. K. Gharachorloo, et al., "Memory Consistency and Event Ordering in Scalable Shared-Memory Multiprocessors", Proc. Int. Symp. On Computer Architecture, May, 1990, p15-24.
4. L. Grate, M. Diekhans, D. Dahle, R. Hughey, Sequence Analysis With the Kestrel SIMD Parallel Processor -1998.
5. S. Hu, W. Shi., Z. Tang.: JIAJIA: An SVM System Based on A New Cache Coherence Protocol. In Proc. of HPCN'99, LNCS 1593, pp. 463-472, April, 1999.
6. W.Hu, W.Shi, "JIAJIA User's Manual", Technical report, Chinese Academy of Sciences, 1999.
7. th ACM SPAA'96, June, 1996, pages 277-287.
8. Lamport L., How to Make a Multiprocessor Computer that Correctly Executes Multiprocess Programs, IEEE Transactions on Computers, 1979, 690-691.
9. K. Li, "Shared Virtual Memory on Loosely Coupled Architectures", PhD Dissertation, Yale University, 1986.
10. W. S. Martins, J. B. Del Cuvillo, F. J. Useche, K. B. Theobald, G. R. Gao, A Multithread Parallel Implementation of a Dynamic Programming Algorithm for Sequence Comparison, Proceedings of the SBAC-PAD, 2001, Pirenopolis, Brazil, p.1-8.
11. R. Melo et al. "Comparing Two Long DNA Sequences Using a DSM System", Proceedings of Euro-Par 2003, p. 517-524, Klagenfurt, 2003.
12. Mosberger D.: Memory Consistency Models, Operating Systems Review, p. 18-26, 1993.
13. Needleman, S. B. and Wunsh. C. D., A General Method Applicable to the Search of Similarities of amino acid sequences of two proteins, J. Mol. Biol., 48:443-453, 1970.
14. G. Pfister, "In Search of Clusters - The Coming Battle for Lowly Parallel Computing", Prentice-Hall, 1995.
15. W. R. Pearson and D. L. Lipman, Improved tools for biological sequence comparison. Proceedings Of The National Academy Of Science USA, v. 85, p. 2444-2448, April 1988
16. J. C. Setubal, J. Meidanis, Introduction to Computational Molecular Biology: Brooks/Cole Publishing Company, 1997.
17. E. Speight, J. Bennet, "Brazos: a Third Generation DSM System", Proc. Of the USENIX/WindowsNT Workshop, p.95-106, August, 1997.
18. T. F. Smith, M. S. Waterman, Identification of common molecular sub-sequences - Journal of Molecular Biology, 147(1) 195-197- 1981.
19. Schwartz, A., et al, PipMaker - A Web Server for Aligning Two Genomic DNA Sequences, Genome Research 10:577-586, April, 2000.