Parallel multiple sequence alignment with dynamic scheduling

International Conference on Information Technology: Coding and Computing, ITCC

Volumn 1, Issue , 2005, Pages 8-13

  Luo, Jiancong ^a   Ahmad, Ishfaq ^a   Ahmed, Munib ^a   Paul, Raymond ^a,b  

^a University of Texas at Arlington   (United States)

^b Office of the Secretary of Defense   (United States)

Author keywords

Dynamic scheduling; Multiple sequence alignment; Parallel computing; Progressive alignment; Task tree

Indexed keywords

DYNAMIC SCHEDULING; MULTIPLE SEQUENCE ALIGNMENT; PROGRESSIVE ALIGNMENT; TASK TREE;

ALGORITHMS; COMPUTATIONAL METHODS; COSTS; LEARNING SYSTEMS; SCHEDULING; TREES (MATHEMATICS);

PARALLEL PROCESSING SYSTEMS;

EID: 24744453521     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (16)

1. 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. Mol. Biol. 48, 443-453, 1970.
2. T. F. Smith and M. S. Waterman, "Identification of Common Molecular Subsequences," J. Mol. Biol. 147, 195-197, 1981.
3. P. Hogeweg and B. Hesper, "The Alignment of Sets of Sequences and the Construction of Phylogenetic Trees: An Integrated Method," J. Mol. Evol. 20, 175-186, 1984.
4. D. F. Feng and R. F. Doolittle, "Progressive Sequence Alignment as A Prerequisite to Correct Phylogenetic Trees," J. Mol. Evol. 25, 351-360, 1987.
5. W. R. Taylor, "A Flexible Method to Align Large Numbers of Biological Sequences," J. Mol. Evol. 28, 161-169, 1988.
6. J. Devereux, P. Haeberli, and O. Smithies, "GCG Package," Nucleic Acids Res. 12, 387-395, 1984.
7. F. Corpet, "Multiple Sequence Alignment with Hierarchical Clustering," Nucleic Acids Res. 16, 10881-10890, 1988.
8. J. Thompson, D. Higgins, and T. Gibson, "CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting Position Specific Gap Penalties and Weight Matrix Choice," Nucleic Acids Res. 22, 673-690, 1994.
9. J. Kim, S. Pramanik, and M. J. Chung, "Multiple Sequence Alignment using Simulated Annealing," Comp. Applic. Biosci. 10(4), 419-426, 1994.
10. M. Ishikawa, T. Toya, M. Hoshida, K. Nitta, A. Ogiwara, and M. Kanehisa, "Multiple Sequence Alignment by Parallel Simulated Annealing," Comp. Applic. Biosci. 9, 267-273, 1993.
11. C. Notredame and D. G. Higgins, "SAGA: Sequence Alignment By Genetic Algorithm," Nucleic Acids Res. 24, 1515-1524, 1996.
12. J. Cheetham, F. Dehne, S. Pitre, A. R. Chaplin, and Taillon P. J., "Parallel CLUSTAL W for PC Clusters," ICCSA 2003, LNCS 2668, pp. 300-309, 2003.
13. U. Catalyurek, M. Gray, T. Kurc, J. Saltz, E. Stahlberg, and R. Ferreira, "A Component-based Implementation of Multiple Sequence," in Proceedings of the 2003 ACM symposium on Applied Computing, March 2003.
14. Y. K. Kwok and I. Ahmad, "Static Scheduling Algorithms for Allocating Directed Task Graphs to Multiprocessors," A CM Computing Surveys, Vol. 31, No. 4, December 1999
15. H.G. Rotithor, "Taxonomy of Dynamic Task Scheduling Schemes in Distributed Computing System," IEE Proceedings Computers and Digital Techniques, Vol. 141, No. 1, January 1994.
16. J. W. Brown, "The Ribonuclease P Database," Nucleic Acids Research, 27:314, 1999. (URL: http://www.mbio.ncsu.edu/RnaseP/home.html)