Abstract
We present the parallel module of a program called LASSAP which is intended to raise numerous limitations of current sequence comparison programs and which is able to handle homologies searches at a large scale level. This module is MIMD oriented, taking advantages of the intrinsic parallelism of most problems. It can run on various architectures (shared memory and message passing) and achieves near perfect speed-up on highly parallel machines (more than 100 processors). Work in progress focus on the way to deal with a network of parallel super-computers, taking advantage of the specificities of each of them.
This research is funded by GREG and Ministry of Research under contract 1410454
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References
S.F Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman. Basic local alignment search tool. J. Mol. Biol., 215:403–410, 1990.
C. Bellanné-Chantelot, B. Lacroix, P. Ougen, A. Billault, S. Beaufils, S. Bertrand, I. Georges, F. Glibert, I. Gros, G. Lucotte, L. Susini, J.J. Codani, P. Gesnouin, S. Pook, G. Vaysseix, T. Ried, J. Lu-Kuo, D. Ward, I. Chumakov, D. Le Paslier, E. Barillot, and D. Cohen. Mapping the whole human genome by fingerprinting yeast artificial chromosomes. Cell, 70:1059–1068, 1992.
Marion L. Blount and Maria Butrico. Dsvm6k: distributed shared virtual memory on the risc system/6000. In '93 Comp Con Conference, pages 491–500, february 1993.
MPI contributors. Mpi: A message passing interface standard. Technical report, MPI committee, 1994.
Al Gesit, Adam Beguelin, Jack Dongarra, Weicheng Jiang, Robert Manchek, and Vaidy Sunderam. Pvm 3 user's guide and reference manual. Technical report, ORNL, may 1994.
G. Gonnet. All against all matching completed at eth zurich. 1991. Electronic mail communication.
P. Keleher, Alan L. Cox, S. Dwarkadas, and W. Zwaenepoel. Treadmarks: Distributed shared memory on standard workstations and operating systems. In Winter Usenix Conference, february 1994.
B. Lacroix and J.J. Codani. Physical mapping of the human genome: computational aspects. In World Scientific, editor, 2nd International Conference on bioinformatics, supercomputing and complex genomes analysis, august 1992.
W.R. Pearson and D.J. Lipman. Improve tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA, 85:2444–2448, 1988.
T.F. Smith and M.S. Watterman. Identification of common molecular subsquences. J. Mol. Biol, 147:195–197, 1981.
Erik L.L. Sonnhammer and D. Kahn. Modular arrangement of proteins as inferred from analysis of homology. Protein Science, 3:482–492, 1994.
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© 1995 Springer-Verlag Berlin Heidelberg
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Codani, JJ., Glemet, E. (1995). Parallelism in LASSAP, a large scale sequence comparisons package. In: Hertzberger, B., Serazzi, G. (eds) High-Performance Computing and Networking. HPCN-Europe 1995. Lecture Notes in Computer Science, vol 919. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0046715
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DOI: https://doi.org/10.1007/BFb0046715
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