Improving performance of multiple sequence alignment analysis in multi-client environments

Proceedings - International Parallel and Distributed Processing Symposium, IPDPS 2002

Volumn , Issue , 2002, Pages 183-

  Catalyurek, U ^a   Stahlberg, E ^b   Ferreira, R ^a   Kurc, T ^a   Saltz, J ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b OHIO SUPERCOMPUTER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84966501422     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPS.2002.1016584     Document Type: Conference Paper

References (19)

1. S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman. Basic local alignment search tool. J. Mol. Biol., 215(3):403-410, Oct 1990.
2. H. Andrade, T. Kurc, A. Sussman, and J. Saltz. Efficient execution of multiple workloads in data analysis applications. In Proceedings of the 2001 ACM/IEEE SC'01 Conference, Denver, CO, Nov. 2001.
3. H. Andrade, T. Kurc, A. Sussman, and J. Saltz. Scheduling multiple data visualization query workloads on a shared memory machine. Technical Report CS-TR-4290 and UMIACS-TR-2001-68, University of Maryland, Department of Computer Science and UMIACS, Oct. 2001. Submitted to IPDPS 2002.
4. M. D. Beynon, T. Kurc, U. Catalyurek, C. Chang, A. Sussman, and J. Saltz. Distributed processing of very large datasets with DataCutter. Parallel Computing, 27(11):1457-1478, Oct. 2001.
5. U. S. Chakravarthy and J. Minker. Multiple query processing in deductive databases using query graphs. In Proceedings of the 12th VLDB Conference, pages 384-391, 1986.
6. F.-C. F. Chen and M. H. Dunham. Common subexpression processing in multiple-query processing. Transactions on Knowledge and Data Engineering, 10(3):493-499, 1998.
7. D.-F. Feng and R. Doolittle. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25:451-360, 1987.
8. J. M. Hellerstein, J. F. Naughton, and A. Pfeffer. Generalized search trees for database systems. In Proc. of 21st International Conference on Very Large Data Bases, Zurich, pages 562-573, September 1995. Available at http://datasplash.cs.berkeley.edu:8000/gist/.
9. D. Higgins and P. Sharp. CLUSTAL : a package for performing multiple sequencealignments on a microcomputer. Gene, 73:237-244, 1988.
10. F. Horn, J. Weare, M. Beukers, S. Hrsch, A. Bairoch, W. Chen, . Edvardsen, F. Campagne, and G. Vriend. Gpcrdb: an information system for g protein-coupled receptors. Nucleic Acids Res., 26(1):277-291, 1998.
11. D. Lipman, S. Altschul, and J. Kececioglu. A tool for multiple sequence alignment. In National Academy Science, volume 86, pages 4412-4415, 1989.
12. D. Mikhailov, H. Cofer, and R. Gomperts. Performance optimizations of Clustal W: Parallel Clustal W, HT Clustal, and MULTICLUSTAL. Technical report, SGI Life and Chemical Sciences, www.sgi.com/solutions/sciences/chembio, 1999.
13. C. Notredame, D. Higgins, and J. Heringa. T-coffee: A novel method for multiple sequence alignments. Journal of Molecular Biology, 302:205-217, 2000.
14. P. Roy, S. Seshadri, S. Sudarshan, and S. Bhobe. Efficient and extensible algorithms for multi query optimization. In Proceedings of the 2000 ACM-SIGMOD Conference, pages 249-260, 2000.
15. N. Saitou and M. Nei. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology Evolution, 4:406-425, 1987.
16. J. Stoye, V. Moulton, and A. Dress. Dca: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. Comput. Appl. Biosci., 13(6):625-626, 1997.
17. J. Thompson, D. Higgins, T.J., and Gibson. Clustal w: improving the sensitivity of progressive multiple alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res, 222:4673-4690, 1994.
18. T. Yap, O. Frieder, and R. Martino. Parallel computation in biological sequence analysis. IEEE Transactions on Parallel and Distributed Systems, 9(3):1-12, 1998.
19. Y. Zhao, P. M. Deshpande, J. F. Naughton, and A. Shukla. Simultaneous optimization and evaluation of multiple dimensional queries. In Proceedings of the 1998 ACM-SIGMOD Conference, pages 271-282, Seattle, WA, 1998.