DNA fragment assembly by ant colony and nearest neighbour heuristics

Authors:
Wannasak Wetcharaporn;Nachol Chaiyaratana;Sissades Tongsima
Affiliations:
Research and Development Center for Intelligent Systems, King Mongkut's Institute of Technology North Bangkok, Bangsue, Bangkok, Thailand;Research and Development Center for Intelligent Systems, King Mongkut's Institute of Technology North Bangkok, Bangsue, Bangkok, Thailand;National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
Venue:
ICAISC'06 Proceedings of the 8th international conference on Artificial Intelligence and Soft Computing
Year:
2006

Citing 6
Cited 1

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Abstract

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.