DNA fragment assembly using an ant colony system algorithm

2003 Congress on Evolutionary Computation, CEC 2003 - Proceedings

Volumn 3, Issue , 2003, Pages 1756-1763

  Meksangsouy, Prakit ^a   Chaiyaratana, Nachol ^a  

^a KING MONGKUT'S UNIVERSITY OF TECHNOLOGY NORTH BANGKOK   (Thailand)

Author keywords

[No Author keywords available]

Indexed keywords

ANT COLONY OPTIMIZATION; ASSEMBLY; COMBINATORIAL OPTIMIZATION; HEURISTIC ALGORITHMS; NUCLEIC ACIDS;

ANT COLONY SYSTEM ALGORITHMS; ASSEMBLY PROBLEMS; CONSENSUS SEQUENCE; DNA FRAGMENT ASSEMBLIES; FRAGMENT ASSEMBLY; NEAREST NEIGHBOUR; OPTIMALITY;

BIOINFORMATICS;

EID: 84901454155     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CEC.2003.1299885     Document Type: Conference Paper

References (17)

1. Allex, C. F., Baldwin, S. F., Sbavlik, J. W. and Blamer, F. R. (1996). Improving the quality of automatic DNA sequence assembly using fluorescent trace-data classifications. Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, St. Louis, MO, 3-14.
2. Applewhite, A. (2002). Mining the genome. IEEE Spectrum, 39(4), 69-71.
3. Beckers, R., Deneubourg, J. L. and Goss, S. (1992). Trails and U-tums in the selection of the shortest path by the ant Lasius Niger. Journal of Theoretical Biology, 159, 397-415.
4. Bonabeau, E., Dorigo, M. and Theraulaz, G. (1999). Swarm intelligence. New York, NY: Oxford University Press.
5. Braga, M. D. V. and Meidanis, J. (2002). An algorithm that builds a set of strings given its overlap graph. Lecture Notes in Computer Science, 2286, 52-63.
6. Burks, C., Engle, M., Forrest, S., Parsons, R. I., Soderlund, C. and Stolorz, P. (1994). Stochastic optimization tools for genomic sequence assembly. In M. D. Adams, C. Fields and J. C. Venter (Eds.), Automated DNA Sequencing and Analvsis Techniques. London, UK Academic Press.
7. Churchill, G., Burks, C., Eggert, M., Engle, M. and Waterman, M. (1993). Assembling DNA sequence fragments by shuffling and simulated annealing, Technical Report LAUR 93-2287, Los Alamos National Lab, Los Alamos, NM.
8. Dorigo, M. and Gambardella, L. M. (1997). Ant colony system: A cooperative learning approach to the traveling salesman problem. IEEE Transactions on Evolutionary, Computation, 1 ( 1), 53-66.
9. Ferreira, C. E., de Souza, C. C. and Wakabayashi, Y. (2002). Rearrangement of DNA fragments: A branchand- cut algorithm. Discrete Applied Mathema/ics, 116( 1 -2), 161- 177.
10. Gambardella, L. M. and Dorigo, M. (2000). An ant colony system hybridized with a new local search for the sequential ordering problem. INFORMS Journal on Computing, 12(3), 237-255.
11. Goldberg, D. E. (1989). Genetic algorithms; In search, optimization and machine learning. Reading, MA: Addison-Wesley.
12. Hodgson, J. (2000). Gene sequencing's industrial revolution. IEEE Spectrum, 37(11), 36-42.
13. Holland, J. H. (1975). Aduptarion in natural and artificial systems. Ann Arbour, MI: University of Michigan Press.
14. Huang, X. (1992). A contig assembly program based on sensitive detection of fragment overlaps. Genomics, 14, 18-25.
15. International Human Genome Sequencing Consortium (2001). Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
16. Parsons, R. J., Forrest, S. and Burks, C. (1995). Genetic algorithms, operators, and DNA fragment assembly. Machine Learning, 21(112), 11-33.
17. Staden, R. (1980). A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acids Research, 8, 3673-3694.