DSAPSO: DNA sequence assembly using continuous particle swarm optimization with smallest position value rule

2012 1st International Conference on Recent Advances in Information Technology, RAIT-2012

Volumn , Issue , 2012, Pages 410-415

  Verma, Ravi Shankar ^a   Kumar, Sanjay ^a  

^a NATIONAL INSTITUTE OF TECHNOLOGY   (India)

Author keywords

Bioinformatics; DNA sequence assembly; Particle Swarm Optimization; PSO; SPV; Swarm Intelligence

Indexed keywords

DISCRETE OPTIMIZATION; DISCRETE OPTIMIZATION PROBLEMS; DNA SEQUENCE ASSEMBLY; PARTICLE SWARM OPTIMIZATION ALGORITHM; POSITION VALUE; PSO; SEQUENTIAL ALGORITHM; SPV; SWARM INTELLIGENCE;

ARTIFICIAL INTELLIGENCE; ASSEMBLY; BIOINFORMATICS; DNA SEQUENCES; GENETIC ALGORITHMS; INFORMATION TECHNOLOGY; MOLECULAR BIOLOGY;

PARTICLE SWARM OPTIMIZATION (PSO);

EID: 84862063752     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/RAIT.2012.6194455     Document Type: Conference Paper

References (22)

1. Kennedy, J. and Eberhart, R. "Particle swarm optimization", Neural Networks, 1995. Proceedings. IEEE International Conference on, Vol. 4, pp. 1942-1948, 1995.
2. Shi, Y. and Eberhart, R. "A modified particle swarm optimizer", Evolutionary Computation Proceedings, 1998. IEEE World Congress on Computational Intelligence. The 1998 IEEE International Conference on, pp. 69-73, 1998.
3. Eberhart, R.C. and Shi, Y. "Comparing inertia weights and constriction factors in particle swarm optimization", Evolutionary Computation, 2000. Proceedings of the 2000 Congress on, Vol. 1, pp. 80-84, 2000.
4. Burks, C. "DNA sequence assembly", Engineering in Medicine and Biology Magazine, IEEE, Vol. 13, pp. 771-773, 1994.
5. P. Green. Phrap. http://www.phrap.org/.
6. G.G. Sutton, O. White, M.D. Adams, and A.R. Kerlavage. "TIGR Assembler: A new tool for assembling large shotgun sequencing projects", Genome Science & Tech., Vol. 1, pp. 9-19, 1995.
7. T. Chen and S. Skiena. "Trie-based data structures for sequence assembly", Combinatorial Pattern Matching, pp. 206-223, 1998.
8. X. Huang and A. Madan. "CAP3: A DNA sequence assembly program", Genome Research, Vol. 9, pp. 868-877, 1999.
9. E.W. Myers. "Towards simplifying and accurately formulating fragment assembly", Journal of Computational Biology, Vol. 2, pp. 275-290, 2000.
10. P.A. Pevzner. "Computational molecular biology: An algorithmic approach", The MIT Press, Vol. 1, 2000.
11. Allex, C.F. and Baldwin, S.F. and Shavlik, J.W. and Blattner, F.R. "Improving the quality of automatic DNA sequence assembly using fluorescent trace-data classifications", Proceedings, Fourth International Conference on Intelligent Systems for Molecular Biology, pp. 3-14, 1996.
12. Wilks, C. and Khuri, S. "A fast shotgun assembly heuristic", Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts, IEEE, pp. 122-123, 2005.
13. Parsons, R. and Forrest, S. and Burks, C. "Genetic algorithms for DNA sequence assembly", Proceedings of the First International Conference on Intelligent Systems for Molecular Biology (ISMB-93), pp. 310-318, 1993.
14. Parsons, R.J. and Forrest, S. and Burks, C. "Genetic algorithms, operators, and DNA fragment assembly", Machine Learning, Vol. 21, pp. 11-33, 1995.
15. Parsons, R.J. and Johnson, M.E. "DNA sequence assembly and genetic algorithms-new results and puzzling insights", Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB-95), pp. 277-284, 1995.
16. Kim, K. and Mohan, CK "Parallel hierarchical adaptive genetic algorithm for fragment assembly", Evolutionary Computation, 2003. CEC'03. The 2003 Congress on, Vol. 1, pp. 600-607, 2003.
17. Fang, S.C. and Wang, Y. and Zhong, J. "A Genetic Algorithm Approach to Solving DNA Fragment Assembly Problem", Journal of Computational and Theoretical Nanoscience, Vol. 2, pp. 499-505, 2005.
18. Kikuchi, S. and Chakraborty, G. "Heuristically tuned GA to solve genome fragment assembly problem", Evolutionary Computation, 2006. CEC 2006. IEEE Congress on, pp. 1491-1498, 2006.
19. Luque, G. and Alba, E. "Metaheuristics for the DNA fragment assembly problem", International Journal of Computational Intelligence Research, Vol. 1, pp. 98-108, 2005.
20. Meksangsouy, P. and Chaiyaratana, N. "DNA fragment assembly using an ant colony system algorithm", Evolutionary Computation, 2003. CEC'03. The 2003 Congress on, Vol. 3, pp. 1756-1763, 2003.
21. Zhao, Y. and Ma, P. and Lan, J. and Liang, C. and Ji, G. "An Improved Ant Colony Algorithm for DNA Sequence Alignment", 2008 International Symposium on Information Science and Engineering, pp. 683-688, 2008.
22. NCBI- http://www.ncbi.nlm.nih.gov/nuccore