The multiple sequence alignment problem in biology
SIAM Journal on Applied Mathematics
A Graph-based Ant system and its convergence
Future Generation Computer Systems
An Ants heuristic for the frequency assignment problem
Future Generation Computer Systems
Parallel ant colonies for the quadratic assignment problem
Future Generation Computer Systems - Special issue on bio-impaired solutions to parallel processing problems
Partitioned optimization algorithms for multiple sequence alignment
AINA '06 Proceedings of the 20th International Conference on Advanced Information Networking and Applications - Volume 02
PROBCONS: probabilistic consistency-based multiple alignment of amino acid sequences
AAAI'04 Proceedings of the 19th national conference on Artifical intelligence
Ant system: optimization by a colony of cooperating agents
IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics
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Multiple sequence alignment is a common task in molecular biology and bioinformatics. Obtaining an accurate alignment of protein sequences is a difficult computational problem because many heuristic techniques cannot achieve optimality in a reasonable running time. A novel multiple sequence alignment algorithm based on ant colony optimization and divide-and-conquer technique is proposed. The algorithm divides a set of sequences into several subsections vertically by bisecting the sequences recursively using the ant colony optimization method. We also present two methods that adaptively adjust the parameters and update the pheromones to avoid local optimal traps. Experimental results show that the algorithm can achieve high quality solution and significantly reduce the running time.