A parallel Smith-Waterman algorithm based on divide and conquer

Proceedings - 5th International Conference on Algorithms and Architectures for Parallel Processing, ICA3PP 2002

Volumn , Issue , 2002, Pages 162-169

  Zhang, Fa ^a   Qiao, Xiang Zhen ^a   Liu, Zhi Yong ^b  

^a INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^b NATIONAL NATURAL SCIENCE FOUNDATION OF CHINA   (China)

Author keywords

biological sequence alignment; divide and conquer; dynamic programming; parallel

Indexed keywords

BIOINFORMATICS; COMPUTER ARCHITECTURE; DYNAMIC PROGRAMMING; MEMORY ARCHITECTURE; MOLECULAR BIOLOGY; PARALLEL ARCHITECTURES;

BIOLOGICAL SEQUENCE ALIGNMENT; BIOLOGICAL SEQUENCES; CRITICAL PROBLEMS; DIVIDE AND CONQUER; MEMORY REQUIREMENTS; PARALLEL; SEQUENCE COMPARISONS; SMITH-WATERMAN ALGORITHM;

ALGORITHMS;

EID: 84964766181     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICAPP.2002.1173568     Document Type: Conference Paper

References (10)

1. S. Aluru, N. Futamura and K. Mehrotra. Parallel Biological Sequence Comparison using Prefix Computations. Proceedings of the 13th International Parallel Processing Symposium and 10th Symposium on Parallel and Distributed Processing, 1998
2. Michael S. Waterman. Introduction to Computational Biology, maps, sequences and genomes. Chapman & Hall, London.1998.
3. David Sankoff, The early introduction of dynamic programming into computational biology. Bioinformatics, vol. 16 no. 1,41-47, 2000.
4. Martin Tompa, Biological Sequence Analysis, Technical Report, Department of Computer Science and Engineering University of Washington, 2000.
5. 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, 48:443-453,1970.
6. T.F. Smith and M.S. Waterman. Identification of common molecular subsequences. Journal of Molecular Biology, 147(1): 195-197.1981.
7. Elizabeth w. Edmiston, Nolan G. Core, Joel H. Saltz and Roger M. Smith. Parallel processing of biological sequence comparison algorithms. International Journal of Parallel Programming, vol. 17, No.3: 259-275, 1988.
8. Eric lander. Protein sequence comparison on a data parallel computer. Proceedings of the 1988 International Conference on Parallel Processing, pages 257-263,1988.
9. Adam R. Galper and Douglas L. Brutlag. Parallel similarity Search and Alignment with the Dynamic Programming Method. Technical Report, Stanford University, California, 1990.
10. Xiangzhen Qiao, Zhao Li and Mingfa Zhu. Parallel computation for Dynamic Programming. 2nd Int. ICSC symposium on computational Intelligence methods & applications (CIMA2001), Bangor, Wales, UK, 2001.