A model to optimize DNA sequences based on particle swarm optimization

Proceedings - 2nd Asia International Conference on Modelling and Simulation, AMS 2008

Volumn , Issue , 2008, Pages 534-539

  Khalid, Noor Khafifah ^a   Kurniawan, Tri Basuki ^a   Ibrahim, Zuwairie ^a   Yusof, Zulkifli Md ^a   Khalid, Marzuki ^a   Engelbrecht, Andries P ^b  

^a UNIVERSITI TEKNOLOGI MALAYSIA   (Malaysia)

^b UNIVERSITY OF PRETORIA   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA PARTICLE SPECTROMETERS; ASSET MANAGEMENT; DESIGN OF EXPERIMENTS; DNA; GENES; NUCLEIC ACIDS; OPTIMIZATION; ORGANIC ACIDS; PARTICLE SPECTROMETERS; PARTICLE SWARM OPTIMIZATION (PSO); TECHNOLOGY;

BIOLOGICAL EXPERIMENTS; DESIGN CONSTRAINTS; DNA NANOTECHNOLOGY; DNA SEQUENCE DESIGN; DNA-BASED COMPUTATION; INTERNATIONAL CONFERENCES; MODELLING AND SIMULATION; PARTICLE SWARM OPTIMIZATIONS; PARTICLE-SWARM OPTIMIZATION; RESEARCH TOPICS; SOCIAL BEHAVIORS; SYSTEMATIC DESIGNS;

DNA SEQUENCES;

EID: 50249158612     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/AMS.2008.25     Document Type: Conference Paper

References (21)

1. Kashiwamura, S., Kameda, A., Yamamoto, M., Ohuchi, A., "Two-step Search for DNA Sequence Design", Proceedings of the 2003 International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC 03), pp. 1815-1818, 2003.
2. M. Arita and S. Kobayashi, " DNA sequence design using templates," New Generation Comput., vol. 20, pp. 263-277, 2002.
3. Kobayashi, S., Kondo, T. "On Template Method for DNA Sequence Design", Preliminary Proceeding of 8th International Meeting on DNA Based Computers, pp.115-124, 2002.
4. C. C. Maley, "DNA computation: Theory, practice, and prospects," Evol.Comput., vol. 6, no. 3, pp. 201-229, 1998.
5. S.Y. Shin, I.H. Lee, D. Kim, B.T. Zhang, "Multiobjective evolutionary optimization of DNA sequences for reliable DNA computing", IEEE Transaction on Evolutionary Computation, Vol. 9, No. 2, 2005, pp. 143-158
6. A. Brenneman and A. Condon, "Strand design for Biomolecular Computation," Theor. Comput. Sci., vol. 287, pp. 39-58, 2002.
7. Seeman, N. C.: De Novo Design of Sequences for Nucleic Acid Structural Engineering. Journal of Biomolecular Structure & Dynamics, 8(3), 573-581, (1990).
8. Baum, E: B.: DNA Sequences Useful for Computation, unpublished, available under http://www.neci.nj.nec.com/homepages/eric/seq.ps (1996)
9. th DIMACS Workshop DNA Based Comput., 1998, pp. 227-235.
10. R. Penchovsky and J. Ackermann, "DNA library design for molecular computation," J. Comput. Bio., vol. 10, no. 2, pp. 215-229, 2003.
11. F. Tanaka, M. Nakatsugawa, M. Yamamoto, T. Shiba, and A. Ohuchi, "Developing support system for sequence design in DNA computing," in Proc. 7th Int. Workshop DNA Based Comput., 2001, pp. 340-349.
12. Marathe, A., Condon, A. E., Corn, R. M.: On Combinatorial DNA Word Design, Proceedings of the 5th International Meeting on DNA Based Computers (1999)
13. U. Feldkamp, S. Saghafi, W. Banzhaf, and H. Rauhe, "DNA sequence generator-A program for the construction of DNA sequences," in Proc. 7th Int. Workshop DNA Based Comput., 2001, pp. 179-188.
14. A. G. Frutos, A. J. Thiel, A. E. Condon, L. M. Smith, and R. M. Corn, "DNA computing at surfaces: Four base mismatch word design," in Proc. 3rd DIMACS Workshop DNA Based Comput., 1997, p. 238.
15. Deaton, R., Murphy, R. C., Rose, J. A., Garzon, M., Franceschetti, D. T., Stevens Jr., S. E.: Genetic Search for Reliable Encodings for DNA-based Computation, First Conference on Genetic Programming (1996)
16. M. Arita, A. Nishikawa, M. Hagiya, K. Komiya, H. Gouzu, and K. Sakamoto, "Improving sequence design for DNA computing," in Proc. Genetic Evol. Comput. Conf. (GECCO), 2000, pp. 875-882.
17. Kennedy, J. and Eberhart, R.C. (1995) Particle Swarm Optimization, Proceeding of IEEE International Conference on Neural Networks. IV. Perth, Australia. Piscataway, N. J.: IEEE Service Center, 1942-1948.
18. Hassan, R., Cohanim, B, and de Weck, O. (2004). A Comparison of Particle Swarm Optimization and the Genetic Algorithm. American Institute of Aeronautics and Astronautics. 1-13.
19. Adriansyah, A. (2007) Particle Swarm Fuzzy Controller for Behavior-Based Mobile Robot. University Technology of Malaysia: PhD Thesis.
20. Santa Lucia, J., Jr. A unified view of polymer, dumbbell, and oligonucleotides DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1998, 1460-1465.
21. L. M. Adleman, "Molecular computation of solutions to combinatorial problems," Science, vol. 266, pp. 1021-1024, 1994.