
This Article  
 
Share  
Bibliographic References  
Add to:  
Digg Furl Spurl Blink Simpy Del.icio.us Y!MyWeb  
Search  
 
ASCII Text  x  
Stjepan Rajko, Srinivas Aluru, "Space and Time Optimal Parallel Sequence Alignments," IEEE Transactions on Parallel and Distributed Systems, vol. 15, no. 12, pp. 10701081, December, 2004.  
BibTex  x  
@article{ 10.1109/TPDS.2004.86, author = {Stjepan Rajko and Srinivas Aluru}, title = {Space and Time Optimal Parallel Sequence Alignments}, journal ={IEEE Transactions on Parallel and Distributed Systems}, volume = {15}, number = {12}, issn = {10459219}, year = {2004}, pages = {10701081}, doi = {http://doi.ieeecomputersociety.org/10.1109/TPDS.2004.86}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE Transactions on Parallel and Distributed Systems TI  Space and Time Optimal Parallel Sequence Alignments IS  12 SN  10459219 SP1070 EP1081 EPD  10701081 A1  Stjepan Rajko, A1  Srinivas Aluru, PY  2004 KW  Computational biology KW  sequence alignments KW  spaceefficient KW  parallel algorithms KW  parallel dynamic programming. VL  15 JA  IEEE Transactions on Parallel and Distributed Systems ER   
Abstract—We present the first space and time optimal parallel algorithm for the pairwise sequence alignment problem, a fundamental problem in computational biology. This problem can be solved sequentially in
[1] S. Aluru, N. Futamura, and K. Mehrotra, “Parallel Biological Sequence Comparison Using Prefix Computations,” J. Parallel and Distributed Computing, vol. 63, no. 3, pp. 264272, 2003.
[2] C.E.R. Alves, E.N. Caceres, and F. Dehne, “Parallel Dynamic Programming for Solving the String Editing Problem on a CGM/BSP,” Proc. ACM Symp. Parallel Algorithms and Architectures, pp. 275281, 2002.
[3] A. Apostolico, M.J. Atallah, L.L. Larmore, and S. MacFaddin, “Efficient Parallel Algorithms for String Editing and Related Problems,” SIAM J. Computing, vol. 19, no. 5, pp. 968988, 1990.
[4] M.O. Dayhoff, R. Schwartz, and B.C. Orcutt, “A Model of Evolutionary Change in Proteins: Matrices for Detecting Distant Relationships,” Atlas of Protein Sequence and Structure, vol. 5, M.O. Dayhoff, ed., Nat'l Biomedical Research Foundation, DC, pp. 345358, 1978.
[5] E.W. Edmiston and R.A. Wagner, “Parallelization of the Dynamic Programming Algorithm for Comparison of Sequences,” Proc. Int'l Conf. Parallel Processing, pp. 7880, 1987.
[6] E.W. Edmiston, N.G. Core, J.H. Saltz, and R.M. Smith, “Parallel Processing of Biological Sequence Comparison Algorithms,” Int'l J. Parallel Programming, vol. 17, no. 3, pp. 259275, 1988.
[7] N. Futamura, S. Aluru, and X. Huang, “Parallel Syntenic Alignments,” Proc. Int'l Conf. High Performance Computing, pp. 420430, 2002.
[8] O. Gotoh, “An Improved Algorithm for Matching Biological Sequences,” J. Molecular Biology, vol. 162, pp. 705708, 1982.
[9] S. Henikoff and J.G. Henikoff, “Amino Acid Substitution Matrices from Protein Blocks,” Proc. Nat'l Academy of Sciences, vol. 89, pp. 1091510919, 1992.
[10] D.S. Hirschberg, “A Linear Space Algorithm for Computing Maximal Common Subsequences,” Comm. ACM, vol. 18, no. 6, pp. 341343, 1975.
[11] A. Grama, V. Kumar, and A. Gupta, Introduction to Parallel Computing, second ed., Reading, Mass.: AddisonWesley Publishing, 2003.
[12] X. Huang, “A SpaceEfficient Parallel Sequence Comparison Algorithm for a MessagePassing Multiprocessor,” Int'l J. Parallel Programming, vol. 18, no. 3, pp. 223239, 1989.
[13] X. Huang, “A SpaceEfficient Algorithm for Local Similarities,” Computer Applications in the Biosciences, vol. 6, no. 4, pp. 373381, 1990.
[14] X. Huang and K. Chao, “A Generalized Global Alignment Algorithm,” Bioinformatics, vol. 19, no. 2, pp. 228233, 2003.
[15] E. Lander, J.P. Mesirov, and W. Taylor, “Protein Sequence Comparison on a Data Parallel Computer,” Proc. Int'l Conf. Parallel Processing, pp. 257263, 1980.
[16] W.J. Masek and M.S. Paterson, “A Faster Algorithm for Computing String Edit Distances,” J. Computer and System Sciences, vol. 20, pp. 1831, 1980.
[17] E.W. Mayers and W. Miller, “Optimal Alignments in Linear Space,” Computer Applications in the Biosciences, vol. 4, no. 1, pp. 1117, 1988.
[18] S.B. Needleman and C.D. Wunsch, “A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins,” J. Molecular Biology, vol. 48, pp. 443453, 1970.
[19] P. Pacheco, Parallel Programming with MPI. San Francisco, Calif.: Morgan Kaufmann Publishers, 1996.
[20] S. Ranka and S. Sahni, “String Editing on an SIMD Hypercube Multicomputer,” J. Parallel and Distributed Computing, vol. 9, pp. 411418, 1990.
[21] J. Setubal and J. Meidanis, Introduction to Computational Molecular Biology. Boston, Mass.: PWS Publishing Company, 1997.
[22] T.F. Smith and M.S. Waterman, “Identification of Common Molecular Subsequences,” J. Molecular Biology, vol. 147, pp. 195197, 1981.