DNA fragment assembly using a grid-based genetic algorithm

Computers and Operations Research

Volumn 35, Issue 9, 2008, Pages 2776-2790

  Nebro, A J ^a   Luque, G ^a   Luna, F ^a   Alba, E ^a  

^a UNIVERSITY OF MÁLAGA   (Spain)

Author keywords

DNA fragment assembly; Genetic algorithm; Grid computing

Indexed keywords

ASYMPTOTIC ANALYSIS; COMBINATORIAL OPTIMIZATION; COMPUTATIONAL COMPLEXITY; FUNCTION EVALUATION; GENES; GENETIC ALGORITHMS; GRID COMPUTING; PARALLEL ALGORITHMS; PROBLEM SOLVING; SCALABILITY;

DNA FRAGMENT ASSEMBLY; GRID METAHEURISTICS; OPTIMAL SOLUTIONS;

DNA SEQUENCES;

EID: 38749086159     PISSN: 03050548     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cor.2006.12.011     Document Type: Article

References (31)

1. Setubal J, Meidanis J. Introduction to computational molecular biology. In: Fragment assembly of DNA. University of Campinas, Brazil; 1997. p. 105-39 [Chapter 4].
2. Green P. Phrap, 2006, 〈http://www.phrap.org/〉.
3. Sutton G, White O, Adams M, Kerlavage A. TIGR assembler: a new tool for assembling large shotgun sequencing projects. Genome Science & Technology 1995; 9-19.
4. Chen T, Skiena S. Trie-based data structure for sequence assembly. In: The eighth symposium on combinatorial pattern matching; 1998. p. 206-23.
5. Huang X., and Madan A. CAP3: a DNA sequence assembly program. Genome Research 9 (1999) 868-877
6. Myers E. Towards simplifying and accurately formulating fragment assembly. Journal of Computational Biology 2 2 (2000) 275-290
7. Pevzner P. Computational molecular biology: an algorithmic approach (2000), The MIT Press, London
8. Davis L. Handbook of genetic algorithms. New York: Van Nostrand Reinhold; 1991.
9. Parsons R., Forrest S., and Burks C. Genetic algorithms, operators, and DNA fragment assembly. Machine Learning 21 (1995) 11-33
10. Bäck T. Fogel DB, Mischalewicz Z, editors. Handbook of evolutionary computation. Oxford: Oxford University Press; 1997.
11. Alba E., and Tomassini M. Parallelism and evolutionary algorithms. IEEE Transactions on Evolutionary Computation 6 5 (2002) 443-462
12. Alba E., and Troya J. A survey of parallel distributed genetic algorithms. Complexity 4 4 (1999) 31-52
13. Berman F, Fox G, Hey A. Grid computing. Making the global infrastructure a reality, communications networking and distributed systems. New York: Wiley; 2003.
14. Abdalhaq B, Cortés A, Margalef T, Luque E. Evolutionary optimization techniques on computational grids. In: ICCS 2002; 2002. p. 513-22.
15. Jing T, Lim M, Ong Y. A parallel hybrid GA for combinatorial optimization using grid technology. In: IEEE congress on evolutionary computation; 2003. p. 1895-902.
16. Imade H, Morishita R, Ono I, Ono N, Okamoto M. A framework of grid-oriented genetic algorithms for large-scale optimization in bioinformatics. In: Proceedings of the 2003 congress on evolutionary computation; 2003. p. 623-30.
17. Eres M, Pound G, Jiao Z, Wason J, Xu F, Keane A, et al. Implementation and utilisation of a grid-enabled problem solving environment in Matlab. Future Generation Computer Systems 2005;21(6):920-9.
18. Lo Presti G, Lo Re G, Storniolo P, Urso A, A grid enabled parallel hybrid genetic algorithm for SPN. In: ICCS 2004, Lecture notes in computer science, vol. 3036. Berlin: Springer; 2004. p. 156-63.
19. Thain D., Tannenbaum T., and Livny M. Condor and the grid. In: Berman F., Fox G., and Hey T. (Eds). Grid computing: making the global infrastructure a reality (2003), Wiley, New York 299-335
20. Linderoth J, Kulkarni S, Goux J, Yoder M. An enabling framework for master-worker applications on the computational grid. In: Proceedings of the ninth IEEE symposium on high performance distributed computing (HPDC), Pittsburg, Pennsylvania; 2000. p. 43-50.
21. Foster I., and Kesselman K. Globus: a metacomputing infrastructure toolkit. International Journal of Supercomputer Applications 11 2 (1997) 115-128
22. Imade H, Morishita R, Ono I, Okamoto M, A grid-oriented genetic algorithm for estimating genetic networks by S-systems. In: Proceedings of the SICE annual conference; 2003. p. 3317-22.
23. Imade H., Morishita R., Ono I., and Ono N. A grid-oriented genetic framework for bioinformatics. New Generation Computing 22 2 (2004) 177-186
24. Imade H, Mizuguchi H, Ono I, Ono N, Okamoto M, "Gridifying" an evolutionary algorithm for inference of genetic networks using the improved GOGA framework and its performance evaluation on OBI grid. In: Grid computing in life science: first international life science grid workshop, LSGRID 2004, Lecture notes in computer science, vol. 3370. Berlin: Springer; 2005. p. 171-86.
25. Hanada Y, Hiroyasu T, Miki M, Okamoto Y, Mega process genetic algorithm using grid MP. In: LSGRID 2004, Lecture notes in bioinformatics, vol. 3370; 2005. p. 152-70.
26. Talbi E.-G. A taxonomy of hybrid metaheuristics. Journal of Heuristics 8 (2002) 807-819
27. Li L, Khuri S. A comparison of DNA fragment assembly algorithms. In: International conference on mathematics and engineering techniques in medicine and biological sciences; 2004. p. 329-35.
28. Grimshaw A, Natrajan A, Humphrey M, Lewis M, Nguyen-Tuong A, Karpovich J, et al. From legion to avaki: the persistence of vision. In: Berman F, Fox G, Hey T, editors. Grid computing: making the global infrastructure a reality. New York: Wiley; 2003. p. 265-98.
29. Frey J, Tannenbaum T, Foster I, Livny M, Tuecke S. Condor-G: a computation management agent for multi-institutional grids. In: Proceedings of the tenth IEEE symposium on high performance distributed computing (HPDC), San Francisco, California; 2001. p. 7-9.
30. Engle M, Burks C. Artificially generated data sets for testing DNA fragment assembly algorithms. Genomics 16.
31. Jing Y, Khuri S. Exact and heuristic algorithms for the DNA fragment assembly problem. In: Proceedings of the IEEE computer society bioinformatics conference. New York: Stanford University, IEEE Press; 2003. p. 581-2.