Space and time optimal parallel sequence alignments

Proceedings of the International Conference on Parallel Processing

Volumn 2003-January, Issue , 2003, Pages 39-47

  Rajko, S ^a   Aluru, S ^b  

^a Iowa State University   (United States)

^b Iowa State University   (United States)

Author keywords

Biology computing; Clustering algorithms; Computational biology; Computer science; Concurrent computing; Dynamic programming; Heuristic algorithms; Parallel algorithms; Read write memory; Sequences

Indexed keywords

ALGORITHMS; ALIGNMENT; BIOINFORMATICS; BIOLOGY; COMPUTER PROGRAMMING; COMPUTER SCIENCE; DYNAMIC PROGRAMMING; HEURISTIC ALGORITHMS; OPTIMIZATION; PARALLEL ALGORITHMS;

BIOLOGY COMPUTING; COMPUTATIONAL BIOLOGY; CONCURRENT COMPUTING; EXPERIMENTAL EVALUATION; OPTIMAL ALGORITHM; PAIRWISE SEQUENCE ALIGNMENT; SEQUENCE ALIGNMENTS; SEQUENCES;

CLUSTERING ALGORITHMS;

EID: 80053279423     PISSN: 01903918     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICPP.2003.1240564     Document Type: Conference Paper

References (22)

1. S. Aluru, N. Futamura and K. Mehrotra, Parallel biological sequence comparison using prefix computations, Journal of Parallel and Distributed Computing, 63(3) (2003) 264-272.
2. C.E.R. Alves, E.N. Caceres, F. Dehne, Parallel Dynamic Programming for Solving the String Editing Problem on a CGM/BSP, ACM Symposium on Parallel Algorithms and Architectures (2002) 275-281.
3. A. Apostolico, M.J. Atallah, L.L. Larmore and S. Macfaddin, Efficient parallel algorithms for string editing and related problems, SIAM Journal of Computing, 19(5) (1990) 968-988.
4. M.O. Dayhoff, R. Schwartz and B.C. Orcutt, A model of evolutionary change in proteins: matrices for detecting distant relationships, In M. O. Dayhoff, (ed.), Atlas of protein sequence and structure, 5, National Biomedical Research Foundation, DC, (1978) 345-358.
5. E.W. Edmiston and R.A. Wagner, Parallelization of the dynamic programming algorithm for comparison of sequences, Proc. International Conference on Parallel Processing (1987) 78-80.
6. 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) (1988) 259-275.
7. N. Futamura, S. Aluru and X. Huang, Parallel syntenic alignments, International Conference on High Performance Computing (2002) 420-430.
8. O. Gotoh, An improved algorithm for matching biological sequences. Journal of Molecular Biology, 162 (1982) 705-708.
9. S. Henikoff and J.G. Henikoff, Amino acid substitution matrices from protein blocks, Proc. National Academy of Sciences, 89 (1992) 10915-10919.
10. D.S. Hirschberg, A linear space algorithm for computing maximal common subsequences, Communications of the ACM, 18(6) (1975) 341-343.
11. A. Grama, V. Kumar, and A. Gupta. Introduction to parallel computing, 2nd ed., Addison-Wesley Publishing, Reading, MA, 2003.
12. X. Huang, A space-efficient parallel sequence comparison algorithm for a message-passing multiprocessor, International Journal of Parallel Programming, 18(3) (1989) 223-239.
13. X. Huang, A space-efficient algorithm for local similarities, Computer Applications in the Biosciences,6(4) (1990) 373-381.
14. X. Huang and K. Chao, A generalized global alignment algorithm, Bioinformatics, 19(2) (2003) 228-233.
15. E. Lander, J.P. Mesirov and W. Taylor, Protein sequence comparison on a data parallel computer, Proc. International Conference on Parallel Processing (1988) 257-263.
16. W.J. Masek and M.S. Paterson, A faster algorithm for computing string edit distances, Journal of Computer and System Sciences, 20 (1980) 18-31.
17. E.W. Mayers and W. Miller, Optimal alignments in linear space, Computer Applications in the Biosciences, 4(1) (1988) 11-17.
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, Journal of Molecular Biology, 48 (1970) 443-453.
19. P. Pacheco. Parallel Programming With MPI, Morgan Kaufmann Publishers, San Francisco, CA, 1996.
20. S. Ranka and S. Sahni, String editing on an SIMD hypercube multicomputer, Journal of Parallel and Distributed Computing, 9 (1990) 411-418.
21. J. Setubal and J. Meidanis, Introduction to computational molecular biology, PWS Publishing Company, Boston, MA, 1997.
22. T.F. Smith and M.S. Waterman, Identification of common molecular subsequences, Journal of Molecular Biology, 147 (1981) 195-197.