Abstract
We present a parallel algorithm for computing an optimal sequence alignment in efficient space. The algorithm is intended for a message-passing architecture with one-dimensional-array topology. The algorithm computes an optimal alignment of two sequences of lengthsM andN inO((M+N) 2/P) time andO((M+N)/P) space per processor, where the number of processors isP>=max(M, N). Thus, whenP=max(M, N) it achieves linear speedup and requires constant space per processor. Some experimental results on an Intel hypercube are provided.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
D. Sankoff and J. B. Kruskal (eds),Time Warps, String Edits, and Macromolecules: the Theory and Practice of Sequence Comparisons, Reading, Massachusetts, Addison-Wesley (1983).
E. W. Edmiston and R. A. Wagner, Parallelization of the Dynamic Programming Algorithm for Comparison of Sequences,Proceedings of the 1987 ICPP, pp. 78–80 (1987).
E. W. Edmiston, N. G. Core, J. H. Saltz, and R. M. Smith, Parallel Processing of Biological Sequence Comparison Algorithms,International Journal of Parallel Programming 17(3):259–275 (1988).
E. Lander, J. P. Mesirov, and W. Taylor, Protein Sequence Comparison on a Data Parallel Computer,Proceedings of the 1988 ICPP 3:257–263 (1988).
R. J. Lipton and D. Lopresti, A Systolic Array for Rapid String Comparison,Proceedings of the 1985 Chapel Hill Conference on VLSI, R. H. Fuchs (ed.), pp. 363–376 (1985).
R. J. Lipton and D. Lopresti, Comparing Long Strings on a Short Systolic Array, Technical Report CS-TR-026-86, Princeton University (1986). Also presented atThe 1986 International Workshop on Systolic Arrays, University of Oxford (1986).
T. F. Smith and M. S. Waterman, Identification of Common Molecular Subsequences,Journal of Molecular Biology 147:195–196 (1981).
O. Gotoh, An Improved Algorithm for Matching Biological Sequences,Journal of Molecular Biology 162:705–708 (1982).
R. A. Wagner and M. J. Fischer, The String-to-String Correction Problem,Journal of the ACM 21(1):168–173 (1974).
S. F. Altschul and B. W. Erickson, Optimal Sequence Alignment Using Affine Gap Costs,Bulletin of Mathematical Biology 48(5):603–616 (1986).
E. W. Myers and W. Miller, Optimal Alignments in Linear Space,Computer Applications in the Biosciences 4(1):11–17 (1988).
D. S. Hirschberg, A Linear Space Algorithm for Computing Maximal Common Subsequences,Communications of the ACM 18(6):341–343 (1975).
Author information
Authors and Affiliations
Additional information
This research was supported by NIH Grant LM05110 from the National Library of Medicine.
Rights and permissions
About this article
Cite this article
Huang, X. A space-efficient parallel sequence comparison algorithm for a message-passing multiprocessor. Int J Parallel Prog 18, 223–239 (1989). https://doi.org/10.1007/BF01407900
Received:
Revised:
Issue Date:
DOI: https://doi.org/10.1007/BF01407900