Parallel strategies for local biological sequence alignment in a cluster of workstations

Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005

Volumn 2005, Issue , 2005, Pages

  Boukerche, Azzedine ^a   De Melo, Alba Cristina Magalhaes Alves ^b   Ayala Rincón, Mauricio ^b   Santana, Thomas Mailleux ^b  

^a UNIVERSITY OF OTTAWA   (Canada)

^b UNIVERSITY OF BRASILIA   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

DISTRIBUTED SHARED MEMORY SYSTEM; DNA SEQUENCING; HEURISTICS; SMITH-WATERMAN ALGORITHM;

ALGORITHMS; DISTRIBUTED DATABASE SYSTEMS; DNA; HEURISTIC METHODS; PARALLEL PROCESSING SYSTEMS; STORAGE ALLOCATION (COMPUTER);

COMPUTER WORKSTATIONS;

EID: 33746314559     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPS.2005.329     Document Type: Conference Paper

References (14)

1. R. B. Batista, D. N. Silva, A. C. M. A. Melo, and L. Weigang. Using a dsm application to locally align dna sequences. In Proc. of the IEEE/ACM Int. Symp. on Cluster Computing and the Grid. IEEE Computer Society, 2004.
2. A. Boukerche, A. C. M. A. Melo, M. E. M. T. Walter, R. C. F. Melo, M. N. P. Santana, and R. B. Batista. Performance evaluation of a local dna sequence alignment algorithm on a cluster of workstations. In Proc. of the Int. Parallel and Distributed Processing Symposium (IPDPS2004). IEEE Society, 2004.
3. Decypher Co. Decypher smith waterman solution, 2003.
4. S. F. Altschul et al. Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Research, 25(17):3389-3402, 1997.
5. DISC group. Smith waterman homology search, 2003.
6. D. S. Hirschberg. Alagorithms for the longest common sequence problem. Journal of the ACM, 24(4): 664-675, 1977.
7. S. Hu, W. Shi, and Z. Tang. Jiajia: An svm system based on a new cache coherence protocol. In High Performance Computing and Networking (HPCN), pages 463-472. Springer-Verlag, April 1999.
8. W. S. Martins, J. B. Del Cuvillo, F. J. Useche, K. B. Theobald, and G. R. Gao. A multithread parallel implementation of a dynamic programming algorithm for sequence comparison. In Symp. on Computer Architecture and HPC (SBAC-PAD), pages 1-8, 2001.
9. R. Melo, M. E. T. Walter, A. C. M. A. Melo, and R. B. Batista. Comparing two long dna sequences using a dsm system. In Euro-Par 2003, pages 517-524. Springer-Verlag, 2003.
10. D. Mosberger. Memory consistency models. Operating Systems Review, pages 18-26, 1993.
11. W. R. Pearson and D. L. Lipman. Improved tools for biological sequence comparison. In Proc. National Academy Of Science, pages 2444-2448. NAS, 1988.
12. G. Pfister. In Search of Clusters - The Coming Battle for Lowly Parallel Computing. Prentice-Hall, 1995.
13. J. C. Setubal and J. Meidanis. Introduction to Computational Molecular Biology. Brooks/Cole Publishing Company, 1997.
14. T. F. Smith and M. S. Waterman. Identification of common molecular sub-sequences. Journal of Molecular Biology, (147):195-197, 1981.