A parallel implementation of the Smith-Waterman algorithm for massive sequences searching

Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings

Volumn 26 IV, Issue , 2004, Pages 2817-2820

  Liao, Hsien Yu ^a   Yin, Meng Lai ^a   Cheng, Yi ^a  

^a CALIFORNIA STATE POLYTECHNIC UNIVERSITY   (United States)

Author keywords

Biological sequence alignment; Massive sequences searching; Parallel processing; Smith Waterman algorithm

Indexed keywords

BIOLOGICAL SEQUENCE ALIGNMENT; MASSIVE SEQUENCE SEARCHING; PARALLEL PROCESSING; SMITH-WATERMAN ALGORITHMS;

ALGORITHMS; BIOLOGICAL MATERIALS; COMPUTATIONAL COMPLEXITY; COSTS; DATABASE SYSTEMS; GENES; MATHEMATICAL TECHNIQUES; PROGRAM COMPILERS;

SENSITIVITY ANALYSIS;

EID: 11144292139     PISSN: 05891019     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (7)

1. T.F Smith and M.S. Waterman, "Identification of common molecular subsequences", Journal of Molecular Biology, 147(1), 195-197, 1981.
2. W.R. Pearson, "Rapid and sensitive comparison with FASTP and FASTA", Methods Enzymol, 183, pp.63-98, 1990.
3. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, "Basic Local Alignment search Tool", J. Mol. Biol., 215, pp.403-410, 1990.
4. Fa Zhang, Xiang-Zhen Qiao, and Zhi-Yong Liu, "A Parallel Smith-Waterman Algorithm Based on Divide Conquer", IEEE Computer Society, 2002.
5. Deshpande AS, Richards DS, and Pearson WR, "A Platform for Biological Sequence Comparison on Parallel Computers", Comput Appl Biosic, 7(2), 237-47, 1991.
6. Gilles Brassard and Paul Bratley, "Algorithmics: Theory & Practice", Prentice Hall, April 1988.
7. Eric V. Denardo, "Dynamic Programming: Models and Applications", Dover Pubns, April 23, 2003.