DNA Fragment Assembly by Ant Colony and Nearest Neighbour Heuristics
This paper presents the use of a combined ant colony system (ACS) and nearest neighbour heuristic (NNH) algorithm in DNA fragment assembly. The assembly process can be treated as combinatorial optimisation where the aim is to find the right order of each fragment in the ordering sequence that leads to the formation of a consensus sequence that truly reflects the original DNA strands. The assembly procedure proposed is composed of two stages: fragment assembly and contiguous sequence (contig) assembly. In the fragment assembly stage, a possible alignment between fragments is determined where the fragment ordering sequence is created using the ACS algorithm. The resulting contigs are then assembled together using the NNH rule. The results indicate that in overall the performance of the combined ACS/NNH technique is superior to that of a standard sequence assembly program (CAP3), which is widely used by many genomic institutions.
KeywordsTravel Salesman Problem Travel Salesman Problem Reverse Complement CAP3 Program Fragment Assembly
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- 4.Green, P.: Phrap documentation. Phred, Phrap, and Consed (2004), http://www.phrap.org
- 9.Burks, C., Engle, M., Forrest, S., Parsons, R., Soderlund, C., Stolorz, P.: Stochastic optimization tools for genomic sequence assembly. In: Adams, M.D., Fields, C., Venter, J.C. (eds.) Automated DNA Sequencing and Analysis, pp. 249–259. Academic Press, London (1994)Google Scholar
- 11.Parsons, R.J., Johnson, M.E.: A case study in experimental design applied to genetic algorithms with applications to DNA sequence assembly. American Journal of Mathematical and Management Sciences 17(3-4), 369–396 (1997)Google Scholar
- 12.Kim, K., Mohan, C.K.: Parallel hierarchical adaptive genetic algorithm for fragment assembly. In: Proceedings of the 2003 Congress on Evolutionary Computation, Canberra, Australia, pp. 600–607 (2003)Google Scholar