DNA fragment assembly using an ant colony system algorithm

This work presents the use of an ant colony system algorithm in a DNA (deoxyribonucleic acid) fragment assembly. The assembly problem is a combinatorial optimisation problem where the aim of the search is to find the right order and orientation of each fragment in the fragment ordering sequence that leads to the formation of a consensus sequence. In this paper, an asymmetric ordering representation is proposed where a path cooperatively generated by all ants in the colony represents the search solution. The optimality of the fragment layout obtained is then determined from the sum of overlap scores calculated for each pair of consecutive fragments in the layout. Two types of assembly problem are investigated: single-contig and multiple-contig problems. The simulation results indicate that in single-contig problems, the performance of the ant colony system algorithm is approximately the same as that of a nearest neighbour heuristic algorithm. On the other hand, the ant colony system algorithm outperforms the nearest neighbour heuristic algorithm when multiple-contig problems are considered.